Starting phenix.real_space_refine on Thu Feb 22 08:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot5_20194/02_2024/6ot5_20194_neut_trim_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians S 80 5.16 5 B 4 2.79 5 C 11664 2.51 5 N 3036 2.21 5 O 3016 1.98 5 H 15620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33420 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 8338 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 611} Chain breaks: 4 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 38, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 399 Chain: "B" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 8338 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 611} Chain breaks: 4 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 38, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 399 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 8338 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 611} Chain breaks: 4 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 38, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 399 Chain: "D" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 8338 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 611} Chain breaks: 4 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2, 'UNK:plan-1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 38, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 399 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.49, per 1000 atoms: 0.43 Number of scatterers: 33420 At special positions: 0 Unit cell: (141.48, 141.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 O 3016 8.00 N 3036 7.00 C 11664 6.00 B 4 5.00 H 15620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.04 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 Atom "HETATM33403 O14 FZ4 C1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33420 O14 FZ4 D1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33369 O14 FZ4 A1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33386 O14 FZ4 B1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.88 Conformation dependent library (CDL) restraints added in 3.8 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 60.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.914A pdb=" N LYS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 181 through 197 removed outlier: 4.037A pdb=" N LYS A 184 " --> pdb=" O PRO A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 423 through 460 removed outlier: 3.522A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 506 removed outlier: 3.897A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 removed outlier: 3.883A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.562A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.951A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 651 through 666 removed outlier: 3.759A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 685 through 705 removed outlier: 3.804A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.726A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.913A pdb=" N LYS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.037A pdb=" N LYS B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 332 through 335 No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 460 removed outlier: 3.522A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 506 removed outlier: 3.897A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 541 removed outlier: 3.883A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.563A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.951A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 651 through 666 removed outlier: 3.759A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 685 through 705 removed outlier: 3.804A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.726A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 removed outlier: 3.914A pdb=" N LYS C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 148 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.037A pdb=" N LYS C 184 " --> pdb=" O PRO C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 332 through 335 No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 423 through 460 removed outlier: 3.522A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 506 removed outlier: 3.897A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 541 removed outlier: 3.883A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.563A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.951A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 651 through 666 removed outlier: 3.759A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 683 Processing helix chain 'C' and resid 685 through 705 removed outlier: 3.804A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.726A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.914A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.037A pdb=" N LYS D 184 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 229 through 237 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 332 through 335 No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 423 through 460 removed outlier: 3.522A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 506 removed outlier: 3.897A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 541 removed outlier: 3.883A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.563A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.951A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 Processing helix chain 'D' and resid 625 through 635 Processing helix chain 'D' and resid 651 through 666 removed outlier: 3.759A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 683 Processing helix chain 'D' and resid 685 through 705 removed outlier: 3.804A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.726A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.688A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= C, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.688A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= E, first strand: chain 'C' and resid 377 through 379 removed outlier: 3.688A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 719 through 722 Processing sheet with id= G, first strand: chain 'D' and resid 377 through 379 removed outlier: 3.688A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 719 through 722 972 hydrogen bonds defined for protein. 2712 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: 12.99 Time building geometry restraints manager: 26.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15608 1.02 - 1.22: 12 1.22 - 1.43: 7696 1.43 - 1.63: 10348 1.63 - 1.83: 128 Bond restraints: 33792 Sorted by residual: bond pdb=" ND2 ASN C 314 " pdb="HD21 ASN C 314 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN D 314 " pdb="HD21 ASN D 314 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 314 " pdb="HD21 ASN B 314 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN D 314 " pdb="HD22 ASN D 314 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN B 314 " pdb="HD22 ASN B 314 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.64: 176 104.64 - 111.99: 36134 111.99 - 119.34: 8830 119.34 - 126.70: 15000 126.70 - 134.05: 224 Bond angle restraints: 60364 Sorted by residual: angle pdb=" N MET A 351 " pdb=" CA MET A 351 " pdb=" C MET A 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.64e+01 angle pdb=" N MET C 351 " pdb=" CA MET C 351 " pdb=" C MET C 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N MET B 351 " pdb=" CA MET B 351 " pdb=" C MET B 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N MET D 351 " pdb=" CA MET D 351 " pdb=" C MET D 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N PHE A 748 " pdb=" CA PHE A 748 " pdb=" C PHE A 748 " ideal model delta sigma weight residual 111.28 114.98 -3.70 1.09e+00 8.42e-01 1.15e+01 ... (remaining 60359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 16021 31.38 - 62.75: 295 62.75 - 94.12: 8 94.12 - 125.50: 0 125.50 - 156.87: 4 Dihedral angle restraints: 16328 sinusoidal: 7632 harmonic: 8696 Sorted by residual: dihedral pdb=" CA VAL A 684 " pdb=" C VAL A 684 " pdb=" N SER A 685 " pdb=" CA SER A 685 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL D 684 " pdb=" C VAL D 684 " pdb=" N SER D 685 " pdb=" CA SER D 685 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL B 684 " pdb=" C VAL B 684 " pdb=" N SER B 685 " pdb=" CA SER B 685 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 16325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1944 0.039 - 0.078: 777 0.078 - 0.117: 243 0.117 - 0.155: 48 0.155 - 0.194: 12 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CG LEU B 425 " pdb=" CB LEU B 425 " pdb=" CD1 LEU B 425 " pdb=" CD2 LEU B 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU C 425 " pdb=" CB LEU C 425 " pdb=" CD1 LEU C 425 " pdb=" CD2 LEU C 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU D 425 " pdb=" CB LEU D 425 " pdb=" CD1 LEU D 425 " pdb=" CD2 LEU D 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 3021 not shown) Planarity restraints: 5468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA B 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA B 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA B 354 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA C 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA C 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA C 354 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA D 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA D 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA D 354 " 0.016 2.00e-02 2.50e+03 ... (remaining 5465 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.67: 16 1.67 - 2.40: 12522 2.40 - 3.13: 93559 3.13 - 3.87: 118056 3.87 - 4.60: 191736 Warning: very small nonbonded interaction distances. Nonbonded interactions: 415889 Sorted by model distance: nonbonded pdb=" HB2 HIS A 426 " pdb=" N17 FZ4 A1001 " model vdw 0.932 2.770 nonbonded pdb=" HB2 HIS D 426 " pdb=" N17 FZ4 D1001 " model vdw 0.933 2.770 nonbonded pdb=" HB2 HIS C 426 " pdb=" N17 FZ4 C1001 " model vdw 0.933 2.770 nonbonded pdb=" HB2 HIS B 426 " pdb=" N17 FZ4 B1001 " model vdw 0.933 2.770 nonbonded pdb="HD11 LEU B 347 " pdb=" HE3 MET B 351 " model vdw 1.448 2.440 ... (remaining 415884 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' } 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: 0.810 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: 0.610 Extract box with map and model: 5.780 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 101.420 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.150 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.009 0.090 18172 Z= 0.625 Angle : 0.856 8.923 24824 Z= 0.460 Chirality : 0.047 0.194 3024 Planarity : 0.005 0.043 3088 Dihedral : 10.202 156.875 5728 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -2.73 (0.15), residues: 2412 helix: -1.57 (0.11), residues: 1536 sheet: -2.03 (0.52), residues: 72 loop : -1.94 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 380 HIS 0.010 0.003 HIS A 426 PHE 0.025 0.003 PHE B 449 TYR 0.030 0.003 TYR D 409 ARG 0.012 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.6823 time to fit residues: 372.5946 Evaluate side-chains 212 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 585 HIS B 314 ASN B 580 GLN B 585 HIS C 314 ASN C 580 GLN C 585 HIS D 314 ASN D 580 GLN D 585 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18172 Z= 0.170 Angle : 0.495 5.168 24824 Z= 0.272 Chirality : 0.033 0.125 3024 Planarity : 0.004 0.044 3088 Dihedral : 5.203 63.460 2660 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.03 % Allowed : 7.44 % Favored : 91.53 % 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: -1.30 (0.16), residues: 2412 helix: -0.31 (0.12), residues: 1608 sheet: -2.70 (0.48), residues: 96 loop : -1.61 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 380 HIS 0.003 0.001 HIS C 160 PHE 0.014 0.001 PHE D 489 TYR 0.011 0.001 TYR B 564 ARG 0.005 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.600 Fit side-chains REVERT: B 598 LEU cc_start: 0.8393 (tt) cc_final: 0.8179 (tp) REVERT: C 371 ARG cc_start: 0.8208 (ttt90) cc_final: 0.8007 (tpt170) REVERT: C 598 LEU cc_start: 0.8389 (tt) cc_final: 0.8174 (tp) REVERT: D 371 ARG cc_start: 0.8206 (ttt90) cc_final: 0.8006 (tpt170) REVERT: D 598 LEU cc_start: 0.8391 (tt) cc_final: 0.8175 (tp) outliers start: 15 outliers final: 15 residues processed: 267 average time/residue: 0.5396 time to fit residues: 228.8082 Evaluate side-chains 231 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN B 735 ASN C 580 GLN C 735 ASN D 580 GLN D 735 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18172 Z= 0.407 Angle : 0.602 4.925 24824 Z= 0.339 Chirality : 0.037 0.133 3024 Planarity : 0.004 0.053 3088 Dihedral : 5.407 69.379 2660 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.34 % Allowed : 8.33 % Favored : 89.33 % 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: -1.08 (0.17), residues: 2412 helix: -0.14 (0.13), residues: 1608 sheet: -1.93 (0.60), residues: 72 loop : -1.65 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.005 0.001 HIS C 301 PHE 0.019 0.002 PHE B 259 TYR 0.027 0.002 TYR D 208 ARG 0.004 0.001 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.848 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: A 631 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6685 (mm-30) REVERT: D 631 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6676 (mm-30) outliers start: 34 outliers final: 26 residues processed: 256 average time/residue: 0.5430 time to fit residues: 221.0079 Evaluate side-chains 234 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 0.4980 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18172 Z= 0.185 Angle : 0.455 4.659 24824 Z= 0.252 Chirality : 0.033 0.118 3024 Planarity : 0.003 0.029 3088 Dihedral : 4.867 64.697 2660 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.58 % Allowed : 10.95 % Favored : 87.47 % 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: -0.35 (0.17), residues: 2412 helix: 0.48 (0.13), residues: 1620 sheet: -0.85 (0.67), residues: 64 loop : -1.68 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.003 0.001 HIS B 301 PHE 0.010 0.001 PHE A 489 TYR 0.015 0.001 TYR C 208 ARG 0.004 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 229 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6693 (mm-30) outliers start: 23 outliers final: 16 residues processed: 240 average time/residue: 0.5299 time to fit residues: 207.5376 Evaluate side-chains 224 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 215 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 580 GLN B 529 GLN B 580 GLN C 580 GLN D 529 GLN D 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18172 Z= 0.218 Angle : 0.463 4.538 24824 Z= 0.255 Chirality : 0.033 0.121 3024 Planarity : 0.003 0.041 3088 Dihedral : 4.720 64.041 2660 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.38 % Allowed : 12.53 % Favored : 86.09 % 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: 0.01 (0.18), residues: 2412 helix: 0.78 (0.13), residues: 1636 sheet: -0.45 (0.72), residues: 64 loop : -1.70 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 380 HIS 0.004 0.001 HIS A 301 PHE 0.015 0.001 PHE A 193 TYR 0.017 0.002 TYR C 208 ARG 0.003 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.772 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 572 MET cc_start: 0.6510 (mmm) cc_final: 0.6303 (mmt) outliers start: 20 outliers final: 16 residues processed: 233 average time/residue: 0.4931 time to fit residues: 189.1996 Evaluate side-chains 226 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 745 HIS B 580 GLN B 745 HIS C 580 GLN C 745 HIS D 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18172 Z= 0.244 Angle : 0.478 4.415 24824 Z= 0.264 Chirality : 0.033 0.119 3024 Planarity : 0.003 0.028 3088 Dihedral : 4.813 66.146 2660 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.86 % Allowed : 13.36 % Favored : 84.78 % 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: 0.18 (0.18), residues: 2412 helix: 0.92 (0.13), residues: 1616 sheet: -0.23 (0.76), residues: 64 loop : -1.61 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 380 HIS 0.004 0.001 HIS A 301 PHE 0.011 0.001 PHE D 441 TYR 0.018 0.002 TYR B 208 ARG 0.002 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 2.330 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 208 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7790 (t80) outliers start: 27 outliers final: 17 residues processed: 257 average time/residue: 0.4903 time to fit residues: 205.6109 Evaluate side-chains 232 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 0.1980 chunk 133 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18172 Z= 0.127 Angle : 0.407 5.079 24824 Z= 0.223 Chirality : 0.032 0.123 3024 Planarity : 0.003 0.024 3088 Dihedral : 4.339 60.189 2660 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.83 % Allowed : 15.29 % Favored : 83.88 % 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: 0.64 (0.18), residues: 2412 helix: 1.30 (0.13), residues: 1636 sheet: 0.13 (0.79), residues: 64 loop : -1.63 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 380 HIS 0.002 0.000 HIS D 160 PHE 0.013 0.001 PHE A 193 TYR 0.011 0.001 TYR C 564 ARG 0.001 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 2.453 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 outliers start: 12 outliers final: 7 residues processed: 215 average time/residue: 0.4897 time to fit residues: 175.0014 Evaluate side-chains 211 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 187 optimal weight: 30.0000 chunk 217 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 735 ASN B 580 GLN C 580 GLN D 745 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18172 Z= 0.337 Angle : 0.529 4.899 24824 Z= 0.292 Chirality : 0.035 0.123 3024 Planarity : 0.004 0.030 3088 Dihedral : 4.854 66.166 2660 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.90 % Allowed : 15.98 % Favored : 83.13 % 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: 0.29 (0.18), residues: 2412 helix: 1.02 (0.13), residues: 1608 sheet: -1.03 (0.60), residues: 96 loop : -1.51 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 380 HIS 0.006 0.001 HIS A 301 PHE 0.012 0.001 PHE B 259 TYR 0.029 0.002 TYR A 208 ARG 0.003 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 2.589 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: A 208 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7818 (t80) REVERT: B 208 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7710 (t80) REVERT: C 208 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 208 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7711 (t80) outliers start: 13 outliers final: 9 residues processed: 222 average time/residue: 0.4864 time to fit residues: 177.5319 Evaluate side-chains 209 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18172 Z= 0.288 Angle : 0.501 4.846 24824 Z= 0.277 Chirality : 0.034 0.120 3024 Planarity : 0.003 0.026 3088 Dihedral : 4.931 67.515 2660 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.17 % Allowed : 15.56 % Favored : 83.26 % 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: 0.17 (0.18), residues: 2412 helix: 0.94 (0.13), residues: 1616 sheet: -1.20 (0.57), residues: 96 loop : -1.57 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 380 HIS 0.005 0.001 HIS C 301 PHE 0.011 0.001 PHE A 441 TYR 0.022 0.002 TYR A 208 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 2.531 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 208 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 208 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7231 (t80) REVERT: C 208 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7232 (t80) REVERT: D 208 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7234 (t80) outliers start: 17 outliers final: 10 residues processed: 210 average time/residue: 0.4730 time to fit residues: 165.5649 Evaluate side-chains 214 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 529 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18172 Z= 0.210 Angle : 0.456 4.687 24824 Z= 0.251 Chirality : 0.033 0.122 3024 Planarity : 0.003 0.024 3088 Dihedral : 4.678 64.530 2660 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.03 % Allowed : 15.70 % Favored : 83.26 % 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: 0.44 (0.18), residues: 2412 helix: 1.15 (0.13), residues: 1612 sheet: -0.92 (0.57), residues: 96 loop : -1.50 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 380 HIS 0.003 0.001 HIS D 301 PHE 0.010 0.001 PHE A 193 TYR 0.017 0.002 TYR A 208 ARG 0.002 0.000 ARG C 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue TYR 359 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 2.704 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: A 208 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 570 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6738 (tm-30) REVERT: B 208 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7180 (t80) REVERT: B 570 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6698 (tm-30) REVERT: C 208 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7098 (t80) REVERT: C 570 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 208 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7107 (t80) REVERT: D 570 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6737 (tm-30) outliers start: 15 outliers final: 11 residues processed: 216 average time/residue: 0.5217 time to fit residues: 188.4963 Evaluate side-chains 219 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144860 restraints weight = 63992.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147325 restraints weight = 45758.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149286 restraints weight = 31894.420| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18172 Z= 0.225 Angle : 0.464 4.699 24824 Z= 0.256 Chirality : 0.033 0.122 3024 Planarity : 0.003 0.025 3088 Dihedral : 4.639 64.263 2660 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.10 % Allowed : 15.91 % Favored : 82.99 % 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: 0.43 (0.18), residues: 2412 helix: 1.14 (0.13), residues: 1612 sheet: -0.80 (0.58), residues: 96 loop : -1.53 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 380 HIS 0.004 0.001 HIS A 301 PHE 0.009 0.001 PHE A 441 TYR 0.019 0.002 TYR A 208 ARG 0.002 0.000 ARG C 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.37 seconds wall clock time: 99 minutes 36.11 seconds (5976.11 seconds total)