Starting phenix.real_space_refine (version: dev) on Tue Feb 28 01:25:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhx_9121/02_2023/6mhx_9121.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "B ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 567": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 698": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 733": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31612 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 8019 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 563 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 410 Chain: "A" Number of atoms: 7787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 7787 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 936 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 19, 'PHE:plan': 8, 'GLU:plan': 41, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 444 Chain: "C" Number of atoms: 7787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 7787 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 936 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 19, 'PHE:plan': 8, 'GLU:plan': 41, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 444 Chain: "D" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 8019 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 563 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 410 Time building chain proxies: 15.47, per 1000 atoms: 0.49 Number of scatterers: 31612 At special positions: 0 Unit cell: (129.95, 132.25, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2902 8.00 N 2874 7.00 C 11132 6.00 H 14648 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.02 Conformation dependent library (CDL) restraints added in 2.9 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 4 sheets defined 67.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.647A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.978A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.656A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.715A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.553A pdb=" N GLN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 462 Processing helix chain 'B' and resid 481 through 508 Processing helix chain 'B' and resid 520 through 542 removed outlier: 4.141A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 567 removed outlier: 3.599A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 610 removed outlier: 4.755A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 707 removed outlier: 4.519A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 147 removed outlier: 4.057A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.608A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.779A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.768A pdb=" N GLN A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 462 Processing helix chain 'A' and resid 481 through 508 Processing helix chain 'A' and resid 520 through 542 removed outlier: 4.208A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.578A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 610 removed outlier: 4.717A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 707 removed outlier: 5.006A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 132 through 147 removed outlier: 4.057A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.608A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.778A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.769A pdb=" N GLN C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 462 Processing helix chain 'C' and resid 481 through 508 Processing helix chain 'C' and resid 520 through 542 removed outlier: 4.208A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 567 removed outlier: 3.579A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 610 removed outlier: 4.717A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 707 removed outlier: 5.005A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.979A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.656A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.715A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.553A pdb=" N GLN D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 462 Processing helix chain 'D' and resid 481 through 508 Processing helix chain 'D' and resid 520 through 542 removed outlier: 4.142A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 567 removed outlier: 3.598A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 610 removed outlier: 4.755A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 707 removed outlier: 4.519A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 Processing sheet with id=AA1, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 378 Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 378 1208 hydrogen bonds defined for protein. 3588 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: 10.84 Time building geometry restraints manager: 26.88 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: 14626 1.02 - 1.22: 22 1.22 - 1.41: 7297 1.41 - 1.61: 9951 1.61 - 1.81: 90 Bond restraints: 31986 Sorted by residual: bond pdb=" C LEU C 707 " pdb=" N PRO C 708 " ideal model delta sigma weight residual 1.326 1.356 -0.029 1.44e-02 4.82e+03 4.16e+00 bond pdb=" C LEU A 707 " pdb=" N PRO A 708 " ideal model delta sigma weight residual 1.326 1.355 -0.028 1.44e-02 4.82e+03 3.91e+00 bond pdb=" C GLY D 383 " pdb=" N PRO D 384 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.60e+00 bond pdb=" C GLY B 383 " pdb=" N PRO B 384 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.25e+00 bond pdb=" C GLY C 383 " pdb=" N PRO C 384 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.19e-02 7.06e+03 2.07e+00 ... (remaining 31981 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.88: 245 105.88 - 112.93: 34697 112.93 - 119.98: 9444 119.98 - 127.03: 12524 127.03 - 134.08: 182 Bond angle restraints: 57092 Sorted by residual: angle pdb=" N VAL A 306 " pdb=" CA VAL A 306 " pdb=" C VAL A 306 " ideal model delta sigma weight residual 110.72 120.40 -9.68 1.01e+00 9.80e-01 9.18e+01 angle pdb=" N VAL C 306 " pdb=" CA VAL C 306 " pdb=" C VAL C 306 " ideal model delta sigma weight residual 110.72 120.31 -9.59 1.01e+00 9.80e-01 9.02e+01 angle pdb=" N THR B 680 " pdb=" CA THR B 680 " pdb=" C THR B 680 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N THR D 680 " pdb=" CA THR D 680 " pdb=" C THR D 680 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N THR C 312 " pdb=" CA THR C 312 " pdb=" C THR C 312 " ideal model delta sigma weight residual 111.28 115.85 -4.57 1.09e+00 8.42e-01 1.76e+01 ... (remaining 57087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.13: 11967 12.13 - 24.26: 978 24.26 - 36.39: 155 36.39 - 48.52: 24 48.52 - 60.65: 8 Dihedral angle restraints: 13132 sinusoidal: 4622 harmonic: 8510 Sorted by residual: dihedral pdb=" CA PHE C 436 " pdb=" C PHE C 436 " pdb=" N ALA C 437 " pdb=" CA ALA C 437 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE A 436 " pdb=" C PHE A 436 " pdb=" N ALA A 437 " pdb=" CA ALA A 437 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE B 436 " pdb=" C PHE B 436 " pdb=" N ALA B 437 " pdb=" CA ALA B 437 " ideal model delta harmonic sigma weight residual 180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 13129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2088 0.035 - 0.071: 640 0.071 - 0.106: 193 0.106 - 0.141: 41 0.141 - 0.176: 6 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA VAL A 306 " pdb=" N VAL A 306 " pdb=" C VAL A 306 " pdb=" CB VAL A 306 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 734 " pdb=" N ILE C 734 " pdb=" C ILE C 734 " pdb=" CB ILE C 734 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2965 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 313 " 0.212 2.00e-02 2.50e+03 2.53e-01 9.57e+02 pdb=" CD GLN A 313 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN A 313 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN A 313 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 313 " -0.382 2.00e-02 2.50e+03 pdb="HE22 GLN A 313 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 313 " 0.211 2.00e-02 2.50e+03 2.52e-01 9.55e+02 pdb=" CD GLN C 313 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 313 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN C 313 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 313 " -0.381 2.00e-02 2.50e+03 pdb="HE22 GLN C 313 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 313 " 0.080 2.00e-02 2.50e+03 8.57e-02 1.10e+02 pdb=" CD GLN B 313 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 313 " -0.075 2.00e-02 2.50e+03 pdb=" NE2 GLN B 313 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 313 " -0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 313 " 0.128 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 195 2.09 - 2.71: 48503 2.71 - 3.34: 87662 3.34 - 3.97: 103139 3.97 - 4.60: 162792 Nonbonded interactions: 402291 Sorted by model distance: nonbonded pdb=" HB3 PHE D 542 " pdb=" HE2 TYR D 544 " model vdw 1.457 2.270 nonbonded pdb=" HB3 PHE B 542 " pdb=" HE2 TYR B 544 " model vdw 1.457 2.270 nonbonded pdb=" HB2 PHE D 542 " pdb=" HD2 TYR D 544 " model vdw 1.557 2.270 nonbonded pdb=" HB2 PHE B 542 " pdb=" HD2 TYR B 544 " model vdw 1.557 2.270 nonbonded pdb="HD11 LEU A 455 " pdb="HD11 LEU A 551 " model vdw 1.634 2.440 ... (remaining 402286 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' and (resid 118 through 187 or (resid 188 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 189 through 213 or (r \ esid 214 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 215 through 216 or (resid 217 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 218 through 239 or (resid 2 \ 40 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 241 through 249 or (resid 250 through 251 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 252 through 278 or (r \ esid 279 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 280 through 318 or (resid 319 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 320 through 322 or (resid 3 \ 23 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 324 through 359 or (resid 360 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 361 through 368 or (resid 369 thr \ ough 372 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 373 through 412 or (resid 413 through 414 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 415 through 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 420 through 534 or (resid 535 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 536 through 538 or (r \ esid 539 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 540 through 547 or (resid 548 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 549 through 552 or (resid 5 \ 53 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 554 through 566 or (resid 567 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 568 through 579 or (resid 580 thr \ ough 581 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 582 through 598 or (resid 599 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 600 through 638 or (resid 6 \ 39 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 640 through 641 or (resid 642 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or resi \ d 643 through 726 or (resid 727 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 728 or (resid 729 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 730 through 744 \ or (resid 745 through 747 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 748 through 756)) selection = (chain 'B' and (resid 118 through 156 or (resid 157 through 159 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 160 throu \ gh 172 or (resid 173 through 174 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 175 through 179 or (resid 180 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 181 \ through 196 or (resid 197 through 198 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 199 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 226 or (resid 227 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 228 through 232 or (resid 233 through 234 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 235 \ through 241 or (resid 242 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 243 through 270 or (resid 271 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 272 throu \ gh 283 or (resid 284 through 286 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 287 through 297 or (resid 298 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 299 \ through 317 or (resid 318 and (name N or name CA or name C or name O or name CB \ or name CG or name H or name HA or name HB2 or name HB3)) or resid 319 through \ 320 or (resid 321 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name \ H or name HA )) or resid 322 through 326 or (resid 327 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 328 through 333 o \ r (resid 334 through 335 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 336 or (resid 337 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 338 through 345 or (res \ id 346 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 347 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 352 through 391 or (resid 392 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 393 through 401 or (resid 402 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 403 through 420 or (resid 421 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 422 through 441 or (resid 442 through 443 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 444 or (resid 445 through 446 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 447 through 491 or (resid 492 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 493 through 504 or (resid 505 throu \ gh 508 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 518 through 531 or (resid 532 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 533 through 540 or (resid 541 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 542 through 588 or (resid 589 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 590 through 604 or (resid 605 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 606 through 618 or (resid 619 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 620 through 642 or (resid 643 through 644 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 645 through 649 or (resid 650 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 651 or (resid 652 through 653 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 654 or (resid 655 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name H or name HA )) or resid 656 or (resid 657 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 658 through 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 671 through 679 or (resid 680 throug \ h 690 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 691 through 705 or (resid 706 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 707 through 713 or (resid 714 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 715 through 718 or (resid 719 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 720 through 721 or (resid 722 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 723 through 746 or (resid 747 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 748 or (resid 749 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 750 through 756)) \ selection = (chain 'C' and (resid 118 through 187 or (resid 188 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 189 through 213 or (r \ esid 214 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 215 through 216 or (resid 217 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 218 through 239 or (resid 2 \ 40 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 241 through 249 or (resid 250 through 251 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 252 through 278 or (r \ esid 279 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 280 through 318 or (resid 319 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 320 through 322 or (resid 3 \ 23 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 324 through 359 or (resid 360 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 361 through 368 or (resid 369 thr \ ough 372 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 373 through 412 or (resid 413 through 414 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 415 through 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 420 through 534 or (resid 535 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 536 through 538 or (r \ esid 539 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 540 through 547 or (resid 548 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 549 through 552 or (resid 5 \ 53 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 554 through 566 or (resid 567 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 568 through 579 or (resid 580 thr \ ough 581 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 582 through 598 or (resid 599 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 600 through 638 or (resid 6 \ 39 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 640 through 641 or (resid 642 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or resi \ d 643 through 726 or (resid 727 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 728 or (resid 729 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 730 through 744 \ or (resid 745 through 747 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 748 through 756)) selection = (chain 'D' and (resid 118 through 156 or (resid 157 through 159 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 160 throu \ gh 172 or (resid 173 through 174 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 175 through 179 or (resid 180 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 181 \ through 196 or (resid 197 through 198 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 199 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 226 or (resid 227 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 228 through 232 or (resid 233 through 234 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 235 \ through 241 or (resid 242 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 243 through 270 or (resid 271 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 272 throu \ gh 283 or (resid 284 through 286 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 287 through 297 or (resid 298 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 299 \ through 317 or (resid 318 and (name N or name CA or name C or name O or name CB \ or name CG or name H or name HA or name HB2 or name HB3)) or resid 319 through \ 320 or (resid 321 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name \ H or name HA )) or resid 322 through 326 or (resid 327 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 328 through 333 o \ r (resid 334 through 335 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 336 or (resid 337 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 338 through 345 or (res \ id 346 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 347 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 352 through 391 or (resid 392 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 393 through 401 or (resid 402 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 403 through 420 or (resid 421 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 422 through 441 or (resid 442 through 443 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 444 or (resid 445 through 446 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 447 through 491 or (resid 492 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 493 through 504 or (resid 505 throu \ gh 508 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 518 through 531 or (resid 532 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 533 through 540 or (resid 541 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 542 through 588 or (resid 589 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 590 through 604 or (resid 605 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 606 through 618 or (resid 619 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 620 through 642 or (resid 643 through 644 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 645 through 649 or (resid 650 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 651 or (resid 652 through 653 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 654 or (resid 655 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name H or name HA )) or resid 656 or (resid 657 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 658 through 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 671 through 679 or (resid 680 throug \ h 690 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 691 through 705 or (resid 706 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 707 through 713 or (resid 714 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 715 through 718 or (resid 719 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 720 through 721 or (resid 722 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 723 through 746 or (resid 747 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 748 or (resid 749 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 750 through 756)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 11132 2.51 5 N 2874 2.21 5 O 2902 1.98 5 H 14648 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.530 Extract box with map and model: 7.570 Check model and map are aligned: 0.430 Process input model: 93.940 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.270 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.004 0.045 17338 Z= 0.290 Angle : 0.670 9.677 23822 Z= 0.421 Chirality : 0.039 0.176 2968 Planarity : 0.004 0.037 2976 Dihedral : 7.565 41.426 5246 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.30 % 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: -2.52 (0.14), residues: 2404 helix: -1.43 (0.10), residues: 1592 sheet: -1.33 (0.54), residues: 76 loop : -1.87 (0.20), residues: 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 458 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 462 average time/residue: 0.5477 time to fit residues: 385.3612 Evaluate side-chains 250 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 645 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 17338 Z= 0.318 Angle : 0.587 5.587 23822 Z= 0.329 Chirality : 0.036 0.156 2968 Planarity : 0.004 0.035 2976 Dihedral : 4.470 23.023 2570 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 1.70 % 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 (0.16), residues: 2404 helix: 0.45 (0.12), residues: 1612 sheet: -0.86 (0.53), residues: 92 loop : -1.81 (0.21), residues: 700 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 271 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 23 outliers final: 9 residues processed: 285 average time/residue: 0.4440 time to fit residues: 210.3495 Evaluate side-chains 239 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3250 time to fit residues: 8.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 645 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17338 Z= 0.182 Angle : 0.483 5.086 23822 Z= 0.268 Chirality : 0.035 0.148 2968 Planarity : 0.003 0.031 2976 Dihedral : 3.996 19.666 2570 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.89 % 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: 1.00 (0.17), residues: 2404 helix: 1.72 (0.13), residues: 1592 sheet: -1.00 (0.48), residues: 100 loop : -1.55 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 257 average time/residue: 0.4653 time to fit residues: 196.3948 Evaluate side-chains 220 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3286 time to fit residues: 8.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS B 313 GLN B 645 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17338 Z= 0.281 Angle : 0.541 5.349 23822 Z= 0.302 Chirality : 0.035 0.142 2968 Planarity : 0.004 0.049 2976 Dihedral : 4.121 19.614 2570 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 1.33 % 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: 1.11 (0.17), residues: 2404 helix: 1.92 (0.13), residues: 1588 sheet: -1.02 (0.49), residues: 100 loop : -1.80 (0.22), residues: 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 235 average time/residue: 0.4614 time to fit residues: 178.0422 Evaluate side-chains 213 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3184 time to fit residues: 7.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.4980 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 17338 Z= 0.167 Angle : 0.467 5.009 23822 Z= 0.258 Chirality : 0.035 0.153 2968 Planarity : 0.003 0.040 2976 Dihedral : 3.799 20.200 2570 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.96 % 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: 1.67 (0.18), residues: 2404 helix: 2.36 (0.13), residues: 1596 sheet: -0.78 (0.49), residues: 100 loop : -1.66 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 243 average time/residue: 0.4587 time to fit residues: 183.8552 Evaluate side-chains 223 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3542 time to fit residues: 8.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17338 Z= 0.246 Angle : 0.503 7.750 23822 Z= 0.281 Chirality : 0.035 0.161 2968 Planarity : 0.003 0.032 2976 Dihedral : 3.847 19.186 2570 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.74 % 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: 1.55 (0.18), residues: 2404 helix: 2.28 (0.13), residues: 1600 sheet: -0.68 (0.48), residues: 100 loop : -1.80 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 225 average time/residue: 0.4559 time to fit residues: 168.9769 Evaluate side-chains 216 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3134 time to fit residues: 5.9844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 197 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17338 Z= 0.275 Angle : 0.528 6.524 23822 Z= 0.296 Chirality : 0.035 0.174 2968 Planarity : 0.003 0.031 2976 Dihedral : 4.019 19.391 2570 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.59 % 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: 1.32 (0.17), residues: 2404 helix: 2.12 (0.13), residues: 1600 sheet: -0.82 (0.47), residues: 100 loop : -1.91 (0.23), residues: 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 224 average time/residue: 0.4530 time to fit residues: 171.2385 Evaluate side-chains 214 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3813 time to fit residues: 6.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 671 ASN C 645 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 17338 Z= 0.133 Angle : 0.461 7.050 23822 Z= 0.249 Chirality : 0.034 0.190 2968 Planarity : 0.002 0.026 2976 Dihedral : 3.599 19.313 2570 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.30 % 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: 1.98 (0.18), residues: 2404 helix: 2.66 (0.13), residues: 1588 sheet: -0.59 (0.46), residues: 100 loop : -1.68 (0.23), residues: 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 2.712 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: 4 outliers final: 4 residues processed: 213 average time/residue: 0.4473 time to fit residues: 159.7376 Evaluate side-chains 208 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3251 time to fit residues: 5.7837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 0.0020 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 645 GLN C 523 HIS C 645 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 17338 Z= 0.140 Angle : 0.461 6.793 23822 Z= 0.248 Chirality : 0.034 0.188 2968 Planarity : 0.002 0.028 2976 Dihedral : 3.472 19.587 2570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.00 % 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: 2.16 (0.18), residues: 2404 helix: 2.80 (0.13), residues: 1592 sheet: -0.41 (0.46), residues: 100 loop : -1.66 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.063 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: 0 outliers final: 0 residues processed: 211 average time/residue: 0.4440 time to fit residues: 158.0036 Evaluate side-chains 205 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17338 Z= 0.190 Angle : 0.490 6.328 23822 Z= 0.265 Chirality : 0.035 0.189 2968 Planarity : 0.003 0.032 2976 Dihedral : 3.533 18.614 2570 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.30 % 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: 2.13 (0.18), residues: 2404 helix: 2.76 (0.13), residues: 1596 sheet: -0.37 (0.46), residues: 100 loop : -1.66 (0.23), residues: 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 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 TYR 321 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 LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 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 LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 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 LYS 500 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 LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 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 ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 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 MET 706 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 LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 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 SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 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 LEU 158 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 SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 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 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 MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 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 LEU 370 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 LYS 376 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 ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 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 MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 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 LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 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 LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 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 LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 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 MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 209 average time/residue: 0.4444 time to fit residues: 157.2060 Evaluate side-chains 206 residues out of total 2152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3629 time to fit residues: 5.1955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN C 645 GLN D 197 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.077180 restraints weight = 190065.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079524 restraints weight = 93805.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.081046 restraints weight = 58413.156| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 17338 Z= 0.133 Angle : 0.468 7.113 23822 Z= 0.247 Chirality : 0.034 0.193 2968 Planarity : 0.002 0.030 2976 Dihedral : 3.365 18.814 2570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.15 % 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: 2.37 (0.18), residues: 2404 helix: 2.93 (0.13), residues: 1596 sheet: -0.29 (0.46), residues: 100 loop : -1.54 (0.24), residues: 708 =============================================================================== Job complete usr+sys time: 5143.74 seconds wall clock time: 93 minutes 0.13 seconds (5580.13 seconds total)