Starting phenix.real_space_refine on Wed Apr 17 04:13:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdm_41168/04_2024/8tdm_41168.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 14658 2.51 5 N 3920 2.21 5 O 4095 1.98 5 H 20279 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A ASP 688": "OD1" <-> "OD2" Residue "B PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 576": "OD1" <-> "OD2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B ASP 688": "OD1" <-> "OD2" Residue "C PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 576": "OD1" <-> "OD2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C ASP 688": "OD1" <-> "OD2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 576": "OD1" <-> "OD2" Residue "D GLU 592": "OE1" <-> "OE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 674": "OE1" <-> "OE2" Residue "D ASP 688": "OD1" <-> "OD2" Residue "E PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 576": "OD1" <-> "OD2" Residue "E GLU 592": "OE1" <-> "OE2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "E GLU 674": "OE1" <-> "OE2" Residue "E ASP 688": "OD1" <-> "OD2" Residue "F PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 576": "OD1" <-> "OD2" Residue "F GLU 592": "OE1" <-> "OE2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "F GLU 674": "OE1" <-> "OE2" Residue "F ASP 688": "OD1" <-> "OD2" Residue "G PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 576": "OD1" <-> "OD2" Residue "G GLU 592": "OE1" <-> "OE2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "G GLU 674": "OE1" <-> "OE2" Residue "G ASP 688": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 43029 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "B" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "C" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "D" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "E" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "F" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Chain: "G" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 6147 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 10, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 512 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 16, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 341 Time building chain proxies: 19.60, per 1000 atoms: 0.46 Number of scatterers: 43029 At special positions: 0 Unit cell: (147.6, 145.2, 141.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 O 4095 8.00 N 3920 7.00 C 14658 6.00 H 20279 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.04 Conformation dependent library (CDL) restraints added in 5.2 seconds 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6426 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 16 sheets defined 69.6% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 166 through 188 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 201 through 232 Processing helix chain 'A' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 482 through 534 Processing helix chain 'A' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 642 through 659 Processing helix chain 'A' and resid 695 through 718 Processing helix chain 'B' and resid 167 through 188 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 201 through 232 Processing helix chain 'B' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 396 Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 482 through 534 Processing helix chain 'B' and resid 537 through 571 removed outlier: 4.125A pdb=" N THR B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 642 through 659 Processing helix chain 'B' and resid 695 through 718 Processing helix chain 'C' and resid 167 through 188 Processing helix chain 'C' and resid 190 through 193 Processing helix chain 'C' and resid 201 through 232 Processing helix chain 'C' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 396 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 451 through 459 Processing helix chain 'C' and resid 460 through 468 Processing helix chain 'C' and resid 482 through 534 Processing helix chain 'C' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 642 through 659 Processing helix chain 'C' and resid 695 through 718 Processing helix chain 'D' and resid 167 through 188 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 201 through 232 Processing helix chain 'D' and resid 236 through 268 removed outlier: 5.026A pdb=" N LYS D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 396 Processing helix chain 'D' and resid 433 through 443 Processing helix chain 'D' and resid 451 through 459 Processing helix chain 'D' and resid 460 through 468 Processing helix chain 'D' and resid 482 through 534 Processing helix chain 'D' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR D 558 " --> pdb=" O ILE D 554 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 642 through 659 Processing helix chain 'D' and resid 695 through 718 Processing helix chain 'E' and resid 167 through 188 Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 201 through 232 Processing helix chain 'E' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS E 248 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS E 279 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP E 319 " --> pdb=" O ASN E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 396 Processing helix chain 'E' and resid 433 through 443 Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'E' and resid 460 through 468 Processing helix chain 'E' and resid 482 through 534 Processing helix chain 'E' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR E 558 " --> pdb=" O ILE E 554 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN E 561 " --> pdb=" O SER E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 616 Processing helix chain 'E' and resid 642 through 659 Processing helix chain 'E' and resid 695 through 718 Processing helix chain 'F' and resid 167 through 188 Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 201 through 232 Processing helix chain 'F' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS F 248 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER F 249 " --> pdb=" O GLY F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS F 279 " --> pdb=" O PRO F 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 396 Processing helix chain 'F' and resid 433 through 443 Processing helix chain 'F' and resid 451 through 459 Processing helix chain 'F' and resid 460 through 468 Processing helix chain 'F' and resid 482 through 534 Processing helix chain 'F' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR F 558 " --> pdb=" O ILE F 554 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN F 561 " --> pdb=" O SER F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 616 Processing helix chain 'F' and resid 642 through 659 Processing helix chain 'F' and resid 695 through 718 Processing helix chain 'G' and resid 167 through 188 Processing helix chain 'G' and resid 190 through 193 Processing helix chain 'G' and resid 201 through 232 Processing helix chain 'G' and resid 236 through 268 removed outlier: 5.027A pdb=" N LYS G 248 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER G 249 " --> pdb=" O GLY G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 334 removed outlier: 3.542A pdb=" N LYS G 279 " --> pdb=" O PRO G 275 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE G 318 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP G 319 " --> pdb=" O ASN G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 396 Processing helix chain 'G' and resid 433 through 443 Processing helix chain 'G' and resid 451 through 459 Processing helix chain 'G' and resid 460 through 468 Processing helix chain 'G' and resid 482 through 534 Processing helix chain 'G' and resid 537 through 571 removed outlier: 4.124A pdb=" N THR G 558 " --> pdb=" O ILE G 554 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN G 561 " --> pdb=" O SER G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 616 Processing helix chain 'G' and resid 642 through 659 Processing helix chain 'G' and resid 695 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.434A pdb=" N VAL A 599 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N MET A 593 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 607 " --> pdb=" O ASN G 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL G 599 " --> pdb=" O GLU G 591 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N MET G 593 " --> pdb=" O THR G 597 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR G 597 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS G 607 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 599 " --> pdb=" O GLU F 591 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N MET F 593 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR F 597 " --> pdb=" O MET F 593 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS F 607 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 599 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET E 593 " --> pdb=" O THR E 597 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR E 597 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS E 607 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 599 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N MET D 593 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS D 607 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 599 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET C 593 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 597 " --> pdb=" O MET C 593 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS C 607 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 599 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET B 593 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS B 607 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS A 680 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LYS A 673 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS A 682 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 671 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA A 684 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A 669 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR A 686 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL A 667 " --> pdb=" O TYR A 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP A 688 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 726 through 731 removed outlier: 6.590A pdb=" N ASP A 727 " --> pdb=" O GLN B 726 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE B 728 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN A 729 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 730 " --> pdb=" O ASN A 729 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR A 731 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP B 727 " --> pdb=" O GLN C 726 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE C 728 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN B 729 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 730 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR B 731 " --> pdb=" O LEU C 730 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 727 " --> pdb=" O GLN D 726 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE D 728 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN C 729 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU D 730 " --> pdb=" O ASN C 729 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR C 731 " --> pdb=" O LEU D 730 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP D 727 " --> pdb=" O GLN E 726 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE E 728 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN D 729 " --> pdb=" O ILE E 728 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU E 730 " --> pdb=" O ASN D 729 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR D 731 " --> pdb=" O LEU E 730 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP E 727 " --> pdb=" O GLN F 726 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE F 728 " --> pdb=" O ASP E 727 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN E 729 " --> pdb=" O ILE F 728 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU F 730 " --> pdb=" O ASN E 729 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR E 731 " --> pdb=" O LEU F 730 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP F 727 " --> pdb=" O GLN G 726 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE G 728 " --> pdb=" O ASP F 727 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN F 729 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU G 730 " --> pdb=" O ASN F 729 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR F 731 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 730 " --> pdb=" O THR G 731 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS B 680 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LYS B 673 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS B 682 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 671 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA B 684 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER B 669 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR B 686 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 667 " --> pdb=" O TYR B 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 688 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'C' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS C 680 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LYS C 673 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 682 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 671 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 684 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER C 669 " --> pdb=" O ALA C 684 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR C 686 " --> pdb=" O VAL C 667 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 667 " --> pdb=" O TYR C 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP C 688 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 195 through 196 Processing sheet with id=AB1, first strand: chain 'D' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS D 680 " --> pdb=" O LYS D 673 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LYS D 673 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS D 682 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 671 " --> pdb=" O LYS D 682 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA D 684 " --> pdb=" O SER D 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER D 669 " --> pdb=" O ALA D 684 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR D 686 " --> pdb=" O VAL D 667 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 667 " --> pdb=" O TYR D 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP D 688 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AB3, first strand: chain 'E' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS E 680 " --> pdb=" O LYS E 673 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LYS E 673 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS E 682 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL E 671 " --> pdb=" O LYS E 682 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA E 684 " --> pdb=" O SER E 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER E 669 " --> pdb=" O ALA E 684 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR E 686 " --> pdb=" O VAL E 667 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL E 667 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP E 688 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 195 through 196 Processing sheet with id=AB5, first strand: chain 'F' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS F 680 " --> pdb=" O LYS F 673 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LYS F 673 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS F 682 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL F 671 " --> pdb=" O LYS F 682 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA F 684 " --> pdb=" O SER F 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER F 669 " --> pdb=" O ALA F 684 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR F 686 " --> pdb=" O VAL F 667 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL F 667 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP F 688 " --> pdb=" O ALA F 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AB7, first strand: chain 'G' and resid 630 through 638 removed outlier: 11.853A pdb=" N LYS G 680 " --> pdb=" O LYS G 673 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LYS G 673 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS G 682 " --> pdb=" O VAL G 671 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL G 671 " --> pdb=" O LYS G 682 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA G 684 " --> pdb=" O SER G 669 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER G 669 " --> pdb=" O ALA G 684 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR G 686 " --> pdb=" O VAL G 667 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL G 667 " --> pdb=" O TYR G 686 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP G 688 " --> pdb=" O ALA G 665 " (cutoff:3.500A) 2035 hydrogen bonds defined for protein. 6018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.96 Time building geometry restraints manager: 36.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20251 1.03 - 1.23: 28 1.23 - 1.42: 9275 1.42 - 1.62: 13713 1.62 - 1.81: 126 Bond restraints: 43393 Sorted by residual: bond pdb=" N THR C 166 " pdb=" CA THR C 166 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N THR D 166 " pdb=" CA THR D 166 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N THR E 166 " pdb=" CA THR E 166 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N THR A 166 " pdb=" CA THR A 166 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N THR G 166 " pdb=" CA THR G 166 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 43388 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 758 107.07 - 113.80: 50514 113.80 - 120.53: 14160 120.53 - 127.26: 12429 127.26 - 133.98: 217 Bond angle restraints: 78078 Sorted by residual: angle pdb=" CB MET C 683 " pdb=" CG MET C 683 " pdb=" SD MET C 683 " ideal model delta sigma weight residual 112.70 119.39 -6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB MET E 683 " pdb=" CG MET E 683 " pdb=" SD MET E 683 " ideal model delta sigma weight residual 112.70 119.38 -6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB MET F 683 " pdb=" CG MET F 683 " pdb=" SD MET F 683 " ideal model delta sigma weight residual 112.70 119.37 -6.67 3.00e+00 1.11e-01 4.94e+00 angle pdb=" CB MET D 683 " pdb=" CG MET D 683 " pdb=" SD MET D 683 " ideal model delta sigma weight residual 112.70 119.37 -6.67 3.00e+00 1.11e-01 4.94e+00 angle pdb=" CB MET B 683 " pdb=" CG MET B 683 " pdb=" SD MET B 683 " ideal model delta sigma weight residual 112.70 119.37 -6.67 3.00e+00 1.11e-01 4.94e+00 ... (remaining 78073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 19242 15.48 - 30.96: 1289 30.96 - 46.44: 259 46.44 - 61.92: 110 61.92 - 77.39: 30 Dihedral angle restraints: 20930 sinusoidal: 9961 harmonic: 10969 Sorted by residual: dihedral pdb=" CB MET D 593 " pdb=" CG MET D 593 " pdb=" SD MET D 593 " pdb=" CE MET D 593 " ideal model delta sinusoidal sigma weight residual -60.00 -111.56 51.56 3 1.50e+01 4.44e-03 9.03e+00 dihedral pdb=" CB MET B 593 " pdb=" CG MET B 593 " pdb=" SD MET B 593 " pdb=" CE MET B 593 " ideal model delta sinusoidal sigma weight residual -60.00 -111.56 51.56 3 1.50e+01 4.44e-03 9.03e+00 dihedral pdb=" CB MET F 593 " pdb=" CG MET F 593 " pdb=" SD MET F 593 " pdb=" CE MET F 593 " ideal model delta sinusoidal sigma weight residual -60.00 -111.56 51.56 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 20927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2798 0.028 - 0.057: 739 0.057 - 0.085: 360 0.085 - 0.113: 135 0.113 - 0.142: 49 Chirality restraints: 4081 Sorted by residual: chirality pdb=" CB ILE E 566 " pdb=" CA ILE E 566 " pdb=" CG1 ILE E 566 " pdb=" CG2 ILE E 566 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB ILE A 566 " pdb=" CA ILE A 566 " pdb=" CG1 ILE A 566 " pdb=" CG2 ILE A 566 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CB ILE B 566 " pdb=" CA ILE B 566 " pdb=" CG1 ILE B 566 " pdb=" CG2 ILE B 566 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 4078 not shown) Planarity restraints: 7161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 610 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO G 611 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO G 611 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 611 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 610 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO C 611 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 611 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 611 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 610 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO D 611 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 611 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 611 " 0.014 5.00e-02 4.00e+02 ... (remaining 7158 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 4391 2.25 - 2.84: 93126 2.84 - 3.43: 108610 3.43 - 4.01: 139145 4.01 - 4.60: 212823 Nonbonded interactions: 558095 Sorted by model distance: nonbonded pdb=" OE1 GLN F 662 " pdb=" H GLN F 662 " model vdw 1.667 1.850 nonbonded pdb=" OE1 GLN B 662 " pdb=" H GLN B 662 " model vdw 1.667 1.850 nonbonded pdb=" OE1 GLN C 662 " pdb=" H GLN C 662 " model vdw 1.667 1.850 nonbonded pdb=" OE1 GLN G 662 " pdb=" H GLN G 662 " model vdw 1.667 1.850 nonbonded pdb=" OE1 GLN D 662 " pdb=" H GLN D 662 " model vdw 1.667 1.850 ... (remaining 558090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.680 Extract box with map and model: 7.450 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 136.050 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23114 Z= 0.130 Angle : 0.437 6.687 31696 Z= 0.237 Chirality : 0.036 0.142 4081 Planarity : 0.003 0.030 3990 Dihedral : 12.359 77.394 7315 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.05 % Allowed : 13.09 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.47 (0.16), residues: 3213 helix: 3.67 (0.11), residues: 2177 sheet: 1.05 (0.31), residues: 273 loop : 1.53 (0.28), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 255 HIS 0.001 0.000 HIS E 689 PHE 0.007 0.001 PHE B 639 TYR 0.005 0.001 TYR E 610 ARG 0.006 0.000 ARG E 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 ILE cc_start: 0.9551 (pt) cc_final: 0.9337 (pt) REVERT: B 634 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 634 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8250 (mm-30) REVERT: D 306 LYS cc_start: 0.8351 (tptp) cc_final: 0.8132 (tptp) REVERT: D 566 ILE cc_start: 0.9544 (pt) cc_final: 0.9260 (pt) REVERT: D 634 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 712 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8468 (ttp-110) REVERT: E 592 GLU cc_start: 0.7609 (tp30) cc_final: 0.7381 (tp30) REVERT: E 634 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8417 (mm-30) REVERT: F 634 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8064 (mm-30) REVERT: F 712 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8427 (ttp-110) REVERT: G 306 LYS cc_start: 0.8337 (tptp) cc_final: 0.8116 (tptp) REVERT: G 683 MET cc_start: 0.8645 (mmm) cc_final: 0.7996 (mpp) outliers start: 1 outliers final: 1 residues processed: 371 average time/residue: 0.6397 time to fit residues: 384.0516 Evaluate side-chains 344 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 551 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 292 optimal weight: 30.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 23114 Z= 0.305 Angle : 0.496 4.478 31696 Z= 0.280 Chirality : 0.037 0.129 4081 Planarity : 0.003 0.036 3990 Dihedral : 3.088 29.597 3362 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.72 % Allowed : 11.26 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.16), residues: 3213 helix: 3.74 (0.11), residues: 2219 sheet: 0.71 (0.32), residues: 273 loop : 0.96 (0.28), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 263 HIS 0.005 0.001 HIS D 668 PHE 0.011 0.001 PHE G 635 TYR 0.013 0.001 TYR E 610 ARG 0.003 0.000 ARG E 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 376 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 343 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8543 (mm-30) REVERT: B 566 ILE cc_start: 0.9597 (pt) cc_final: 0.9393 (pt) REVERT: B 634 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 634 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8463 (mm-30) REVERT: D 566 ILE cc_start: 0.9584 (pt) cc_final: 0.9336 (pt) REVERT: E 593 MET cc_start: 0.8639 (mmm) cc_final: 0.8262 (mtt) REVERT: E 610 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: E 634 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8570 (mm-30) REVERT: F 634 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8337 (mm-30) REVERT: G 593 MET cc_start: 0.8414 (mmm) cc_final: 0.8164 (mtt) outliers start: 33 outliers final: 21 residues processed: 358 average time/residue: 0.6391 time to fit residues: 374.2521 Evaluate side-chains 352 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 330 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 292 optimal weight: 40.0000 chunk 316 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23114 Z= 0.268 Angle : 0.475 5.500 31696 Z= 0.270 Chirality : 0.037 0.137 4081 Planarity : 0.003 0.035 3990 Dihedral : 3.104 13.915 3360 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.35 % Allowed : 9.80 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.15), residues: 3213 helix: 3.81 (0.11), residues: 2212 sheet: 0.20 (0.31), residues: 273 loop : 0.91 (0.27), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 263 HIS 0.007 0.001 HIS D 689 PHE 0.013 0.001 PHE D 267 TYR 0.007 0.001 TYR G 610 ARG 0.005 0.000 ARG E 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 330 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 720 ASP cc_start: 0.8468 (t0) cc_final: 0.8125 (t0) REVERT: B 634 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8540 (mm-30) REVERT: C 634 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8473 (mm-30) REVERT: C 655 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: E 593 MET cc_start: 0.8827 (mmm) cc_final: 0.8564 (mtt) REVERT: E 610 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: E 634 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8592 (mm-30) REVERT: F 634 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8358 (mm-30) outliers start: 45 outliers final: 25 residues processed: 340 average time/residue: 0.6666 time to fit residues: 379.3588 Evaluate side-chains 347 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 320 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 311 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 278 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23114 Z= 0.309 Angle : 0.478 4.619 31696 Z= 0.273 Chirality : 0.037 0.141 4081 Planarity : 0.003 0.038 3990 Dihedral : 3.173 14.153 3360 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.19 % Allowed : 10.06 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.30 (0.15), residues: 3213 helix: 3.80 (0.10), residues: 2212 sheet: -0.05 (0.30), residues: 273 loop : 0.86 (0.27), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 263 HIS 0.006 0.001 HIS D 689 PHE 0.013 0.001 PHE B 563 TYR 0.011 0.001 TYR C 610 ARG 0.003 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 313 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8548 (t0) cc_final: 0.8195 (t0) REVERT: B 634 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8607 (mm-30) REVERT: C 634 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8553 (mm-30) REVERT: C 655 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: E 610 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: E 634 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8640 (mm-30) REVERT: F 634 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8431 (mm-30) REVERT: G 504 ASN cc_start: 0.8990 (m110) cc_final: 0.8676 (m110) outliers start: 42 outliers final: 35 residues processed: 326 average time/residue: 0.5942 time to fit residues: 328.7930 Evaluate side-chains 337 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 300 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 263 TRP Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 231 optimal weight: 30.0000 chunk 128 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 215 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23114 Z= 0.181 Angle : 0.437 5.090 31696 Z= 0.245 Chirality : 0.036 0.136 4081 Planarity : 0.003 0.039 3990 Dihedral : 3.149 14.392 3360 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.19 % Allowed : 10.48 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.15), residues: 3213 helix: 3.92 (0.10), residues: 2212 sheet: 0.20 (0.32), residues: 259 loop : 0.80 (0.27), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 263 HIS 0.006 0.001 HIS D 689 PHE 0.011 0.001 PHE B 267 TYR 0.008 0.001 TYR G 610 ARG 0.003 0.000 ARG F 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 323 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8557 (t0) cc_final: 0.8188 (t0) REVERT: C 634 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8514 (mm-30) REVERT: D 588 MET cc_start: 0.8970 (ptp) cc_final: 0.8759 (ptp) REVERT: E 610 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: E 634 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8503 (mm-30) REVERT: F 634 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8410 (mm-30) REVERT: G 504 ASN cc_start: 0.9028 (m110) cc_final: 0.8709 (m110) REVERT: G 566 ILE cc_start: 0.9647 (pt) cc_final: 0.9446 (pt) REVERT: G 634 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8601 (mm-30) outliers start: 42 outliers final: 37 residues processed: 335 average time/residue: 0.5766 time to fit residues: 329.1478 Evaluate side-chains 349 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 311 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 311 optimal weight: 0.6980 chunk 258 optimal weight: 0.3980 chunk 144 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23114 Z= 0.133 Angle : 0.429 7.114 31696 Z= 0.237 Chirality : 0.037 0.148 4081 Planarity : 0.003 0.039 3990 Dihedral : 3.110 14.458 3360 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.88 % Allowed : 10.90 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.61 (0.15), residues: 3213 helix: 4.01 (0.10), residues: 2212 sheet: 0.32 (0.33), residues: 259 loop : 0.91 (0.28), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 255 HIS 0.005 0.001 HIS D 689 PHE 0.008 0.001 PHE B 563 TYR 0.007 0.001 TYR G 610 ARG 0.004 0.000 ARG F 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 331 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8422 (t0) cc_final: 0.8080 (t0) REVERT: B 593 MET cc_start: 0.8656 (mmm) cc_final: 0.8286 (mtt) REVERT: C 634 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8515 (mm-30) REVERT: D 588 MET cc_start: 0.8949 (ptp) cc_final: 0.8744 (ptp) REVERT: D 592 GLU cc_start: 0.7615 (tp30) cc_final: 0.7411 (tp30) REVERT: D 683 MET cc_start: 0.8563 (mmm) cc_final: 0.8050 (mmm) REVERT: E 610 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: E 634 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8482 (mm-30) REVERT: F 634 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8403 (mm-30) REVERT: G 504 ASN cc_start: 0.9028 (m110) cc_final: 0.8693 (m110) REVERT: G 634 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8591 (mm-30) REVERT: G 713 MET cc_start: 0.8943 (mtp) cc_final: 0.8659 (mtp) outliers start: 36 outliers final: 31 residues processed: 341 average time/residue: 0.5974 time to fit residues: 347.1273 Evaluate side-chains 349 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 317 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 553 PHE Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 177 optimal weight: 0.0870 chunk 227 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 189 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN C 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23114 Z= 0.175 Angle : 0.436 4.991 31696 Z= 0.242 Chirality : 0.036 0.135 4081 Planarity : 0.003 0.037 3990 Dihedral : 3.087 14.501 3360 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.03 % Allowed : 11.11 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.15), residues: 3213 helix: 4.03 (0.10), residues: 2212 sheet: 0.15 (0.32), residues: 273 loop : 0.97 (0.28), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 255 HIS 0.004 0.001 HIS D 689 PHE 0.007 0.001 PHE B 563 TYR 0.007 0.001 TYR C 610 ARG 0.004 0.000 ARG F 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 317 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8471 (t0) cc_final: 0.8121 (t0) REVERT: C 634 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8550 (mm-30) REVERT: D 588 MET cc_start: 0.8966 (ptp) cc_final: 0.8754 (ptp) REVERT: E 588 MET cc_start: 0.8910 (ptp) cc_final: 0.8639 (ptp) REVERT: E 610 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: E 634 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8478 (mm-30) REVERT: F 588 MET cc_start: 0.8986 (ptp) cc_final: 0.8750 (ptp) REVERT: F 634 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8425 (mm-30) REVERT: G 504 ASN cc_start: 0.9062 (m110) cc_final: 0.8723 (m110) outliers start: 39 outliers final: 33 residues processed: 330 average time/residue: 0.5969 time to fit residues: 335.7418 Evaluate side-chains 342 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 308 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 553 PHE Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 553 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23114 Z= 0.320 Angle : 0.489 5.387 31696 Z= 0.276 Chirality : 0.037 0.137 4081 Planarity : 0.003 0.036 3990 Dihedral : 3.145 14.382 3360 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.03 % Allowed : 11.52 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.15), residues: 3213 helix: 3.94 (0.10), residues: 2212 sheet: -0.07 (0.32), residues: 273 loop : 0.79 (0.27), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 263 HIS 0.005 0.001 HIS C 668 PHE 0.014 0.001 PHE E 563 TYR 0.017 0.001 TYR C 610 ARG 0.004 0.000 ARG F 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 304 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8565 (t0) cc_final: 0.8219 (t0) REVERT: B 720 ASP cc_start: 0.8654 (t0) cc_final: 0.8269 (t0) REVERT: E 588 MET cc_start: 0.8966 (ptp) cc_final: 0.8687 (ptp) REVERT: E 610 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: E 634 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8516 (mm-30) REVERT: F 634 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8473 (mm-30) REVERT: G 504 ASN cc_start: 0.9097 (m110) cc_final: 0.8600 (m110) outliers start: 39 outliers final: 37 residues processed: 317 average time/residue: 0.5860 time to fit residues: 317.7617 Evaluate side-chains 336 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 553 PHE Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 553 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 50.0000 chunk 271 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 ASN ** E 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23114 Z= 0.201 Angle : 0.454 5.546 31696 Z= 0.253 Chirality : 0.037 0.165 4081 Planarity : 0.003 0.036 3990 Dihedral : 3.175 14.524 3360 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.82 % Allowed : 11.52 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.16), residues: 3213 helix: 3.99 (0.10), residues: 2212 sheet: -0.01 (0.32), residues: 273 loop : 0.85 (0.28), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 255 HIS 0.005 0.001 HIS A 689 PHE 0.012 0.001 PHE F 563 TYR 0.011 0.001 TYR C 610 ARG 0.005 0.000 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 307 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8525 (t0) cc_final: 0.8176 (t0) REVERT: B 720 ASP cc_start: 0.8625 (t0) cc_final: 0.8253 (t0) REVERT: E 588 MET cc_start: 0.8930 (ptp) cc_final: 0.8668 (ptp) REVERT: E 610 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: E 634 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8488 (mm-30) REVERT: F 634 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8436 (mm-30) outliers start: 35 outliers final: 34 residues processed: 314 average time/residue: 0.6461 time to fit residues: 344.6235 Evaluate side-chains 339 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 304 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 553 PHE Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 553 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 2.9990 chunk 186 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 295 optimal weight: 50.0000 chunk 255 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23114 Z= 0.235 Angle : 0.467 6.071 31696 Z= 0.261 Chirality : 0.036 0.159 4081 Planarity : 0.003 0.036 3990 Dihedral : 3.169 14.460 3360 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.88 % Allowed : 11.52 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.16), residues: 3213 helix: 3.95 (0.10), residues: 2212 sheet: -0.03 (0.33), residues: 273 loop : 0.79 (0.28), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 255 HIS 0.005 0.001 HIS C 689 PHE 0.012 0.001 PHE F 563 TYR 0.012 0.001 TYR C 610 ARG 0.006 0.000 ARG D 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue SER 324 is missing expected H atoms. Skipping. Residue VAL 325 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue LEU 331 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue VAL 392 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Residue MET 394 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue TYR 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue VAL 442 is missing expected H atoms. Skipping. Residue TYR 449 is missing expected H atoms. Skipping. Residue ILE 450 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue LEU 456 is missing expected H atoms. Skipping. Residue MET 459 is missing expected H atoms. Skipping. Residue ILE 460 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue VAL 464 is missing expected H atoms. Skipping. Residue LEU 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue VAL 492 is missing expected H atoms. Skipping. Residue TYR 493 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue SER 495 is missing expected H atoms. Skipping. Residue LEU 499 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 ASP cc_start: 0.8571 (t0) cc_final: 0.8235 (t0) REVERT: B 720 ASP cc_start: 0.8719 (t0) cc_final: 0.8361 (t0) REVERT: E 588 MET cc_start: 0.8955 (ptp) cc_final: 0.8685 (ptp) REVERT: E 610 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: E 634 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8494 (mm-30) REVERT: F 634 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8458 (mm-30) outliers start: 36 outliers final: 35 residues processed: 314 average time/residue: 0.5870 time to fit residues: 311.8452 Evaluate side-chains 340 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 501 HIS Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 553 PHE Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 553 PHE Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 501 HIS Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain G residue 553 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 235 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 224 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067916 restraints weight = 245288.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070238 restraints weight = 91915.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071632 restraints weight = 47896.192| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23114 Z= 0.174 Angle : 0.452 6.185 31696 Z= 0.249 Chirality : 0.037 0.155 4081 Planarity : 0.003 0.052 3990 Dihedral : 3.170 14.695 3360 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.82 % Allowed : 11.63 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.16), residues: 3213 helix: 4.01 (0.10), residues: 2212 sheet: 0.02 (0.33), residues: 273 loop : 0.89 (0.28), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 255 HIS 0.005 0.001 HIS A 689 PHE 0.010 0.001 PHE F 563 TYR 0.010 0.001 TYR C 610 ARG 0.004 0.000 ARG F 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7446.77 seconds wall clock time: 137 minutes 41.92 seconds (8261.92 seconds total)