Starting phenix.real_space_refine (version: dev) on Sun May 15 05:10:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwi_7299/05_2022/6bwi_7299_updated.pdb" } resolution = 3.7 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= 0.000 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 882": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A GLU 1169": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 601": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 955": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 1062": "NH1" <-> "NH2" Residue "B ARG 1166": "NH1" <-> "NH2" Residue "B GLU 1169": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 601": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 882": "NH1" <-> "NH2" Residue "C ARG 892": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 1062": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "C ARG 1166": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D ARG 601": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Residue "D PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 882": "NH1" <-> "NH2" Residue "D ARG 892": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D ARG 1062": "NH1" <-> "NH2" Residue "D ARG 1166": "NH1" <-> "NH2" Residue "D GLU 1169": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23491 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 435 Chain: "B" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 440 Chain: "C" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5644 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 440 Chain: "D" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 5649 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 24, 'TRANS': 791} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TYR:plan': 3, 'UNK:plan-1': 195, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 435 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 228 Unusual residues: {' NA': 3, 'Y01': 6, 'NAG': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 227 Unusual residues: {' NA': 2, 'Y01': 6, 'NAG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'Y01': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {'Y01': 7, 'NAG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 13.97, per 1000 atoms: 0.59 Number of scatterers: 23491 At special positions: 0 Unit cell: (131.61, 131.61, 153.75, 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 92 16.00 Na 5 11.00 O 4020 8.00 N 4064 7.00 C 15310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.18 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=1.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=1.51 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=1.54 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=4, symmetry=0 Links applied NAG-ASN " NAG A1210 " - " ASN A 992 " " NAG B1209 " - " ASN B 992 " " NAG D1208 " - " ASN D 992 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 2.9 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 4 sheets defined 74.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 13 through 25 Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 54 through 63 removed outlier: 4.042A pdb=" N UNK A 58 " --> pdb=" O UNK A 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK A 59 " --> pdb=" O UNK A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 205 through 216 removed outlier: 5.305A pdb=" N UNK A 213 " --> pdb=" O UNK A 209 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N UNK A 214 " --> pdb=" O UNK A 210 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N UNK A 215 " --> pdb=" O UNK A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.709A pdb=" N UNK A 232 " --> pdb=" O UNK A 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK A 233 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 261 through 275 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 420 through 431 removed outlier: 5.076A pdb=" N GLU A 426 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 431 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.907A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 537 through 545 removed outlier: 3.574A pdb=" N THR A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.779A pdb=" N TRP A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 585 through 593 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 611 through 633 removed outlier: 4.728A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 657 removed outlier: 3.691A pdb=" N LEU A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 653 through 657' Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 690 through 697 removed outlier: 4.067A pdb=" N PHE A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 769 through 775 removed outlier: 4.019A pdb=" N PHE A 773 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 775 " --> pdb=" O TRP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 802 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.835A pdb=" N PHE A 819 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 820 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 821 " --> pdb=" O TYR A 818 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 822 " --> pdb=" O PHE A 819 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 829 " --> pdb=" O CYS A 826 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 831 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.550A pdb=" N LEU A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 911 removed outlier: 3.888A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 951 removed outlier: 3.774A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 930 " --> pdb=" O MET A 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 Processing helix chain 'A' and resid 1018 through 1030 Processing helix chain 'A' and resid 1036 through 1067 removed outlier: 4.285A pdb=" N ALA A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A1049 " --> pdb=" O TYR A1045 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1091 removed outlier: 4.645A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1138 removed outlier: 4.000A pdb=" N ALA A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1171 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 54 through 63 removed outlier: 4.043A pdb=" N UNK B 58 " --> pdb=" O UNK B 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK B 59 " --> pdb=" O UNK B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 205 through 216 removed outlier: 5.306A pdb=" N UNK B 213 " --> pdb=" O UNK B 209 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N UNK B 214 " --> pdb=" O UNK B 210 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N UNK B 215 " --> pdb=" O UNK B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.709A pdb=" N UNK B 232 " --> pdb=" O UNK B 229 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK B 233 " --> pdb=" O UNK B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 261 through 275 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 420 through 431 removed outlier: 5.075A pdb=" N GLU B 426 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET B 430 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 431 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.906A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 537 through 545 removed outlier: 3.574A pdb=" N THR B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 removed outlier: 3.778A pdb=" N TRP B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'B' and resid 596 through 601 Processing helix chain 'B' and resid 611 through 633 removed outlier: 4.728A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 657 removed outlier: 3.691A pdb=" N LEU B 657 " --> pdb=" O THR B 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 653 through 657' Processing helix chain 'B' and resid 664 through 667 No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 673 through 680 Processing helix chain 'B' and resid 690 through 697 removed outlier: 4.042A pdb=" N PHE B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 702 No H-bonds generated for 'chain 'B' and resid 699 through 702' Processing helix chain 'B' and resid 769 through 775 removed outlier: 4.019A pdb=" N PHE B 773 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 775 " --> pdb=" O TRP B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 802 Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.834A pdb=" N PHE B 819 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP B 820 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 821 " --> pdb=" O TYR B 818 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 822 " --> pdb=" O PHE B 819 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 829 " --> pdb=" O CYS B 826 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 831 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.550A pdb=" N LEU B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 911 removed outlier: 3.836A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 951 removed outlier: 3.775A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET B 927 " --> pdb=" O VAL B 923 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS B 928 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 929 " --> pdb=" O LYS B 925 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 930 " --> pdb=" O MET B 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 942 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 949 " --> pdb=" O GLY B 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 951 " --> pdb=" O ALA B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 1018 through 1033 removed outlier: 3.550A pdb=" N ASN B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1070 removed outlier: 4.285A pdb=" N ALA B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B1049 " --> pdb=" O TYR B1045 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1091 removed outlier: 4.645A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1138 removed outlier: 3.999A pdb=" N ALA B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1171 Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 54 through 63 removed outlier: 4.043A pdb=" N UNK C 58 " --> pdb=" O UNK C 54 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK C 59 " --> pdb=" O UNK C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 205 through 216 removed outlier: 5.305A pdb=" N UNK C 213 " --> pdb=" O UNK C 209 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N UNK C 214 " --> pdb=" O UNK C 210 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N UNK C 215 " --> pdb=" O UNK C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.708A pdb=" N UNK C 232 " --> pdb=" O UNK C 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK C 233 " --> pdb=" O UNK C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 261 through 275 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 420 through 431 removed outlier: 5.076A pdb=" N GLU C 426 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 430 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 431 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.907A pdb=" N ALA C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 537 through 545 removed outlier: 3.575A pdb=" N THR C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 removed outlier: 3.779A pdb=" N TRP C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 586 through 593 Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 611 through 633 removed outlier: 4.727A pdb=" N ALA C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 657 removed outlier: 3.691A pdb=" N LEU C 657 " --> pdb=" O THR C 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 653 through 657' Processing helix chain 'C' and resid 664 through 667 No H-bonds generated for 'chain 'C' and resid 664 through 667' Processing helix chain 'C' and resid 673 through 680 Processing helix chain 'C' and resid 690 through 697 removed outlier: 4.045A pdb=" N PHE C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 702 No H-bonds generated for 'chain 'C' and resid 699 through 702' Processing helix chain 'C' and resid 769 through 775 removed outlier: 4.018A pdb=" N PHE C 773 " --> pdb=" O ARG C 770 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 775 " --> pdb=" O TRP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 802 Processing helix chain 'C' and resid 814 through 831 removed outlier: 3.835A pdb=" N PHE C 819 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP C 820 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 821 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 822 " --> pdb=" O PHE C 819 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 829 " --> pdb=" O CYS C 826 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 831 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 859 Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.550A pdb=" N LEU C 877 " --> pdb=" O THR C 873 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 911 removed outlier: 3.836A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 951 removed outlier: 3.774A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C 927 " --> pdb=" O VAL C 923 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS C 928 " --> pdb=" O SER C 924 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 929 " --> pdb=" O LYS C 925 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 930 " --> pdb=" O MET C 926 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL C 942 " --> pdb=" O GLY C 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 949 " --> pdb=" O GLY C 945 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 1018 through 1030 Processing helix chain 'C' and resid 1036 through 1069 removed outlier: 4.286A pdb=" N ALA C1041 " --> pdb=" O ASN C1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS C1049 " --> pdb=" O TYR C1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1091 removed outlier: 4.646A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1138 removed outlier: 4.000A pdb=" N ALA C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1171 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 54 through 63 removed outlier: 4.042A pdb=" N UNK D 58 " --> pdb=" O UNK D 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N UNK D 59 " --> pdb=" O UNK D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 205 through 216 removed outlier: 5.306A pdb=" N UNK D 213 " --> pdb=" O UNK D 209 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N UNK D 214 " --> pdb=" O UNK D 210 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N UNK D 215 " --> pdb=" O UNK D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.708A pdb=" N UNK D 232 " --> pdb=" O UNK D 229 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNK D 233 " --> pdb=" O UNK D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 406 through 411 Processing helix chain 'D' and resid 420 through 431 removed outlier: 5.076A pdb=" N GLU D 426 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D 430 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP D 431 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.907A pdb=" N ALA D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 537 through 545 removed outlier: 3.575A pdb=" N THR D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 removed outlier: 3.778A pdb=" N TRP D 565 " --> pdb=" O ASP D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 586 through 593 Processing helix chain 'D' and resid 596 through 601 Processing helix chain 'D' and resid 611 through 633 removed outlier: 4.728A pdb=" N ALA D 616 " --> pdb=" O ARG D 612 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.691A pdb=" N LEU D 657 " --> pdb=" O THR D 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 653 through 657' Processing helix chain 'D' and resid 664 through 667 No H-bonds generated for 'chain 'D' and resid 664 through 667' Processing helix chain 'D' and resid 673 through 680 Processing helix chain 'D' and resid 690 through 697 removed outlier: 4.048A pdb=" N PHE D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 702 No H-bonds generated for 'chain 'D' and resid 699 through 702' Processing helix chain 'D' and resid 769 through 775 removed outlier: 4.018A pdb=" N PHE D 773 " --> pdb=" O ARG D 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 775 " --> pdb=" O TRP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 802 Processing helix chain 'D' and resid 814 through 831 removed outlier: 3.834A pdb=" N PHE D 819 " --> pdb=" O LEU D 816 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP D 820 " --> pdb=" O LEU D 817 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 821 " --> pdb=" O TYR D 818 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 822 " --> pdb=" O PHE D 819 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 829 " --> pdb=" O CYS D 826 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN D 831 " --> pdb=" O GLU D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 859 Processing helix chain 'D' and resid 866 through 883 removed outlier: 3.550A pdb=" N LEU D 877 " --> pdb=" O THR D 873 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 911 removed outlier: 3.836A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 911 " --> pdb=" O LEU D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 951 removed outlier: 3.775A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET D 927 " --> pdb=" O VAL D 923 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS D 928 " --> pdb=" O SER D 924 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP D 929 " --> pdb=" O LYS D 925 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 930 " --> pdb=" O MET D 926 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 942 " --> pdb=" O GLY D 938 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY D 950 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 951 " --> pdb=" O ALA D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 965 Processing helix chain 'D' and resid 1018 through 1030 Processing helix chain 'D' and resid 1036 through 1067 removed outlier: 4.286A pdb=" N ALA D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS D1049 " --> pdb=" O TYR D1045 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1091 removed outlier: 4.646A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1138 removed outlier: 4.000A pdb=" N ALA D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1171 Processing sheet with id= A, first strand: chain 'A' and resid 101 through 103 Processing sheet with id= B, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= C, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'D' and resid 101 through 103 1056 hydrogen bonds defined for protein. 2928 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: 7.14 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6784 1.33 - 1.45: 4014 1.45 - 1.57: 13032 1.57 - 1.69: 2 1.69 - 1.81: 136 Bond restraints: 23968 Sorted by residual: bond pdb=" C GLU B1169 " pdb=" N GLN B1170 " ideal model delta sigma weight residual 1.334 1.590 -0.256 1.33e-02 5.65e+03 3.70e+02 bond pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 1.334 1.588 -0.254 1.32e-02 5.74e+03 3.70e+02 bond pdb=" C LEU B1162 " pdb=" N GLY B1163 " ideal model delta sigma weight residual 1.334 1.560 -0.226 1.32e-02 5.74e+03 2.92e+02 bond pdb=" C GLU A1169 " pdb=" N GLN A1170 " ideal model delta sigma weight residual 1.334 1.542 -0.208 1.33e-02 5.65e+03 2.43e+02 bond pdb=" C GLU D1169 " pdb=" N GLN D1170 " ideal model delta sigma weight residual 1.334 1.527 -0.192 1.33e-02 5.65e+03 2.09e+02 ... (remaining 23963 not shown) Histogram of bond angle deviations from ideal: 94.95 - 103.58: 308 103.58 - 112.20: 12479 112.20 - 120.83: 13057 120.83 - 129.45: 6810 129.45 - 138.07: 206 Bond angle restraints: 32860 Sorted by residual: angle pdb=" C LEU A1162 " pdb=" N GLY A1163 " pdb=" CA GLY A1163 " ideal model delta sigma weight residual 119.98 137.85 -17.87 1.11e+00 8.12e-01 2.59e+02 angle pdb=" O LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 122.12 108.93 13.19 1.06e+00 8.90e-01 1.55e+02 angle pdb=" CA LEU A1162 " pdb=" C LEU A1162 " pdb=" N GLY A1163 " ideal model delta sigma weight residual 117.22 130.77 -13.55 1.17e+00 7.31e-01 1.34e+02 angle pdb=" C LEU B1162 " pdb=" N GLY B1163 " pdb=" CA GLY B1163 " ideal model delta sigma weight residual 119.98 132.24 -12.26 1.11e+00 8.12e-01 1.22e+02 angle pdb=" N PRO C 701 " pdb=" CA PRO C 701 " pdb=" CB PRO C 701 " ideal model delta sigma weight residual 103.25 113.65 -10.40 1.05e+00 9.07e-01 9.82e+01 ... (remaining 32855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 12824 15.58 - 31.16: 762 31.16 - 46.74: 194 46.74 - 62.32: 49 62.32 - 77.90: 15 Dihedral angle restraints: 13844 sinusoidal: 4300 harmonic: 9544 Sorted by residual: dihedral pdb=" CA UNK A 93 " pdb=" C UNK A 93 " pdb=" N UNK A 94 " pdb=" CA UNK A 94 " ideal model delta harmonic sigma weight residual -180.00 -138.03 -41.97 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA UNK D 93 " pdb=" C UNK D 93 " pdb=" N UNK D 94 " pdb=" CA UNK D 94 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 dihedral pdb=" CA UNK B 93 " pdb=" C UNK B 93 " pdb=" N UNK B 94 " pdb=" CA UNK B 94 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 13841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3921 0.224 - 0.447: 75 0.447 - 0.671: 16 0.671 - 0.894: 2 0.894 - 1.118: 1 Chirality restraints: 4015 Sorted by residual: chirality pdb=" C1 NAG D1208 " pdb=" ND2 ASN D 992 " pdb=" C2 NAG D1208 " pdb=" O5 NAG D1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" C1 NAG B1209 " pdb=" ND2 ASN B 992 " pdb=" C2 NAG B1209 " pdb=" O5 NAG B1209 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG A1210 " pdb=" ND2 ASN A 992 " pdb=" C2 NAG A1210 " pdb=" O5 NAG A1210 " both_signs ideal model delta sigma weight residual False -2.40 -3.07 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 4012 not shown) Planarity restraints: 4065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 992 " 0.561 2.00e-02 2.50e+03 5.54e-01 3.84e+03 pdb=" CG ASN A 992 " -0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 992 " 0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN A 992 " -1.003 2.00e-02 2.50e+03 pdb=" C1 NAG A1210 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 992 " 0.490 2.00e-02 2.50e+03 4.96e-01 3.07e+03 pdb=" CG ASN D 992 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN D 992 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN D 992 " -0.890 2.00e-02 2.50e+03 pdb=" C1 NAG D1208 " 0.414 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 992 " -0.422 2.00e-02 2.50e+03 4.71e-01 2.77e+03 pdb=" CG ASN B 992 " 0.126 2.00e-02 2.50e+03 pdb=" OD1 ASN B 992 " -0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN B 992 " 0.831 2.00e-02 2.50e+03 pdb=" C1 NAG B1209 " -0.466 2.00e-02 2.50e+03 ... (remaining 4062 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 53 2.38 - 3.01: 12068 3.01 - 3.64: 34721 3.64 - 4.27: 49745 4.27 - 4.90: 79058 Nonbonded interactions: 175645 Sorted by model distance: nonbonded pdb=" CG ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.745 2.616 nonbonded pdb=" OD1 ASN B 992 " pdb=" O1 NAG B1209 " model vdw 1.857 2.440 nonbonded pdb=" O PHE D 975 " pdb=" N GLN D 977 " model vdw 1.917 2.520 nonbonded pdb=" CE3 TRP B 864 " pdb=" CAR Y01 B1207 " model vdw 1.975 2.992 nonbonded pdb=" CG ASN A 992 " pdb=" O1 NAG A1210 " model vdw 2.091 2.616 ... (remaining 175640 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 1 through 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) selection = (chain 'B' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'C' and (resid 1 through 1174 or resid 1204 through 1205)) selection = (chain 'D' and (resid 1 through 989 or (resid 990 and (name N or name CA or name \ C or name O or name CB )) or resid 991 through 1174 or resid 1204 through 1205) \ ) } 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 92 5.16 5 Na 5 4.78 5 C 15310 2.51 5 N 4064 2.21 5 O 4020 1.98 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.970 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.210 Process input model: 58.390 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.011 0.256 23968 Z= 0.698 Angle : 1.387 17.867 32860 Z= 0.729 Chirality : 0.085 1.118 4015 Planarity : 0.012 0.288 4062 Dihedral : 12.080 77.900 7552 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.11 % Favored : 91.52 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -5.08 (0.14), residues: 2428 helix: -3.41 (0.08), residues: 1572 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 856 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 661 time to evaluate : 2.452 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 677 average time/residue: 0.3786 time to fit residues: 378.7751 Evaluate side-chains 367 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3609 time to fit residues: 8.5709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN A 990 HIS ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS C1164 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 977 GLN D1032 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.8296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.500 23968 Z= 5.711 Angle : 4.991 47.406 32860 Z= 2.368 Chirality : 0.269 1.837 4015 Planarity : 0.031 0.255 4062 Dihedral : 17.640 101.123 3756 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 104.68 Ramachandran Plot: Outliers : 10.09 % Allowed : 26.57 % Favored : 63.34 % Rotamer Outliers : 21.17 % Cbeta Deviations : 4.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 5.85 % 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: -8.03 (0.08), residues: 2428 helix: -4.90 (0.06), residues: 1672 sheet: None (None), residues: 0 loop : -5.88 (0.14), residues: 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 204 time to evaluate : 2.480 Fit side-chains outliers start: 373 outliers final: 245 residues processed: 542 average time/residue: 0.3352 time to fit residues: 290.2535 Evaluate side-chains 431 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 186 time to evaluate : 2.520 Switching outliers to nearest non-outliers outliers start: 245 outliers final: 0 residues processed: 245 average time/residue: 0.2425 time to fit residues: 110.5157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 462 GLN A 656 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 462 GLN C 656 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 GLN ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 ASN D 462 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.8865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.501 23968 Z= 5.680 Angle : 4.966 46.184 32860 Z= 2.358 Chirality : 0.267 1.670 4015 Planarity : 0.031 0.271 4062 Dihedral : 18.570 110.193 3756 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 110.16 Ramachandran Plot: Outliers : 7.54 % Allowed : 39.91 % Favored : 52.55 % Rotamer Outliers : 26.67 % Cbeta Deviations : 3.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.38 % Twisted General : 7.12 % 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: -8.45 (0.08), residues: 2428 helix: -5.09 (0.05), residues: 1648 sheet: None (None), residues: 0 loop : -6.39 (0.12), residues: 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 470 poor density : 182 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 470 outliers final: 294 residues processed: 602 average time/residue: 0.3185 time to fit residues: 304.5848 Evaluate side-chains 466 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 172 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 294 outliers final: 0 residues processed: 294 average time/residue: 0.2192 time to fit residues: 120.8153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.9128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.499 23968 Z= 5.670 Angle : 4.948 46.068 32860 Z= 2.352 Chirality : 0.267 1.732 4015 Planarity : 0.031 0.285 4062 Dihedral : 18.833 108.282 3756 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 112.11 Ramachandran Plot: Outliers : 7.41 % Allowed : 40.98 % Favored : 51.61 % Rotamer Outliers : 25.77 % Cbeta Deviations : 3.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.42 % Twisted General : 7.88 % 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: -8.53 (0.07), residues: 2428 helix: -5.12 (0.05), residues: 1664 sheet: None (None), residues: 0 loop : -6.48 (0.10), residues: 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 454 poor density : 179 time to evaluate : 2.381 Fit side-chains outliers start: 454 outliers final: 299 residues processed: 597 average time/residue: 0.3420 time to fit residues: 316.6795 Evaluate side-chains 478 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 179 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 299 outliers final: 0 residues processed: 299 average time/residue: 0.2382 time to fit residues: 127.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.9285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.500 23968 Z= 5.668 Angle : 4.962 46.202 32860 Z= 2.353 Chirality : 0.269 1.776 4015 Planarity : 0.030 0.209 4062 Dihedral : 18.972 105.491 3756 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 112.89 Ramachandran Plot: Outliers : 7.04 % Allowed : 42.96 % Favored : 50.00 % Rotamer Outliers : 23.44 % Cbeta Deviations : 3.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.42 % Twisted General : 8.18 % 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: -8.55 (0.07), residues: 2428 helix: -5.15 (0.05), residues: 1696 sheet: None (None), residues: 0 loop : -6.45 (0.11), residues: 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 170 time to evaluate : 2.659 Fit side-chains outliers start: 413 outliers final: 258 residues processed: 561 average time/residue: 0.3436 time to fit residues: 298.8686 Evaluate side-chains 437 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 179 time to evaluate : 2.338 Switching outliers to nearest non-outliers outliers start: 258 outliers final: 0 residues processed: 258 average time/residue: 0.2320 time to fit residues: 109.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 GLN B1070 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.499 23968 Z= 5.661 Angle : 4.940 46.063 32860 Z= 2.349 Chirality : 0.269 1.836 4015 Planarity : 0.030 0.193 4062 Dihedral : 19.085 107.618 3756 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 112.77 Ramachandran Plot: Outliers : 7.00 % Allowed : 43.86 % Favored : 49.14 % Rotamer Outliers : 20.77 % Cbeta Deviations : 3.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.46 % Twisted General : 8.64 % 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: -8.56 (0.07), residues: 2428 helix: -5.16 (0.05), residues: 1688 sheet: None (None), residues: 0 loop : -6.47 (0.11), residues: 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 172 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 366 outliers final: 226 residues processed: 516 average time/residue: 0.3693 time to fit residues: 289.6373 Evaluate side-chains 406 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 180 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 226 outliers final: 0 residues processed: 226 average time/residue: 0.2404 time to fit residues: 98.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 866 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.502 23968 Z= 5.674 Angle : 4.954 46.039 32860 Z= 2.357 Chirality : 0.271 1.858 4015 Planarity : 0.031 0.306 4062 Dihedral : 19.109 107.291 3756 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 113.35 Ramachandran Plot: Outliers : 6.71 % Allowed : 44.15 % Favored : 49.14 % Rotamer Outliers : 13.68 % Cbeta Deviations : 3.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.46 % Twisted General : 8.43 % 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: -8.62 (0.07), residues: 2428 helix: -5.17 (0.05), residues: 1712 sheet: None (None), residues: 0 loop : -6.59 (0.11), residues: 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 172 time to evaluate : 2.283 Fit side-chains outliers start: 241 outliers final: 139 residues processed: 396 average time/residue: 0.3539 time to fit residues: 217.2840 Evaluate side-chains 309 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 170 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 0 residues processed: 139 average time/residue: 0.2410 time to fit residues: 62.5512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.9425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.088 0.497 23968 Z= 5.680 Angle : 4.957 45.934 32860 Z= 2.359 Chirality : 0.271 1.871 4015 Planarity : 0.030 0.238 4062 Dihedral : 19.102 106.364 3756 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 113.08 Ramachandran Plot: Outliers : 6.71 % Allowed : 45.43 % Favored : 47.86 % Rotamer Outliers : 12.71 % Cbeta Deviations : 3.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.46 % Twisted General : 8.73 % 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: -8.61 (0.07), residues: 2428 helix: -5.17 (0.05), residues: 1644 sheet: None (None), residues: 0 loop : -6.56 (0.10), residues: 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 173 time to evaluate : 2.239 Fit side-chains revert: symmetry clash outliers start: 224 outliers final: 128 residues processed: 387 average time/residue: 0.3268 time to fit residues: 199.8792 Evaluate side-chains 308 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 180 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 0 residues processed: 128 average time/residue: 0.2111 time to fit residues: 53.0428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.498 23968 Z= 5.689 Angle : 4.955 45.920 32860 Z= 2.362 Chirality : 0.272 1.855 4015 Planarity : 0.030 0.258 4062 Dihedral : 19.141 106.327 3756 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 112.83 Ramachandran Plot: Outliers : 6.71 % Allowed : 45.18 % Favored : 48.11 % Rotamer Outliers : 9.19 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.58 % Twisted General : 8.69 % 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: -8.64 (0.07), residues: 2428 helix: -5.19 (0.05), residues: 1680 sheet: None (None), residues: 0 loop : -6.57 (0.11), residues: 748 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 177 time to evaluate : 2.361 Fit side-chains revert: symmetry clash outliers start: 162 outliers final: 84 residues processed: 319 average time/residue: 0.3561 time to fit residues: 176.0127 Evaluate side-chains 267 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 183 time to evaluate : 2.285 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.2299 time to fit residues: 37.6365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 ASN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.498 23968 Z= 5.691 Angle : 4.959 45.906 32860 Z= 2.365 Chirality : 0.274 1.860 4015 Planarity : 0.032 0.295 4062 Dihedral : 19.188 106.156 3756 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 112.88 Ramachandran Plot: Outliers : 6.80 % Allowed : 45.55 % Favored : 47.65 % Rotamer Outliers : 4.31 % Cbeta Deviations : 3.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.46 % Twisted General : 8.94 % 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: -8.66 (0.07), residues: 2428 helix: -5.20 (0.05), residues: 1676 sheet: None (None), residues: 0 loop : -6.59 (0.11), residues: 752 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 184 time to evaluate : 2.358 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 35 residues processed: 251 average time/residue: 0.3206 time to fit residues: 130.0439 Evaluate side-chains 219 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2563 time to fit residues: 21.1792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 ASN C 866 GLN ** C 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.094140 restraints weight = 52208.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.092353 restraints weight = 63746.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092857 restraints weight = 78121.670| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.9468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.089 0.501 23968 Z= 5.693 Angle : 4.948 45.897 32860 Z= 2.362 Chirality : 0.273 1.864 4015 Planarity : 0.031 0.265 4062 Dihedral : 19.180 106.317 3756 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 113.22 Ramachandran Plot: Outliers : 6.63 % Allowed : 45.68 % Favored : 47.69 % Rotamer Outliers : 4.99 % Cbeta Deviations : 3.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 8.86 % 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: -8.67 (0.07), residues: 2428 helix: -5.21 (0.05), residues: 1688 sheet: None (None), residues: 0 loop : -6.62 (0.11), residues: 740 =============================================================================== Job complete usr+sys time: 9436.21 seconds wall clock time: 167 minutes 19.44 seconds (10039.44 seconds total)