Starting phenix.real_space_refine (version: dev) on Thu Dec 15 00:04:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/12_2022/6bwd_7297_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/12_2022/6bwd_7297.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/6bwd_7297/12_2022/6bwd_7297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/12_2022/6bwd_7297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/12_2022/6bwd_7297_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwd_7297/12_2022/6bwd_7297_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= 0.006 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 455": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 681": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 770": "NH1" <-> "NH2" Residue "C ARG 853": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 681": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 856": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23187 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5613 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 227} Link IDs: {'CIS': 48, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5618 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 226} Link IDs: {'CIS': 47, 'PTRANS': 27, 'TRANS': 696} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5628 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 223} Link IDs: {'CIS': 45, 'PTRANS': 27, 'TRANS': 698} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 640 Unresolved non-hydrogen angles: 867 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 326 Chain: "D" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5593 Classifications: {'peptide': 771} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 232} Link IDs: {'CIS': 46, 'PTRANS': 27, 'TRANS': 697} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 674 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 6, 'UNK:plan-1': 121, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 212 Unusual residues: {' MG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 142 Unusual residues: {' MG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 280 Unusual residues: {'Y01': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' MG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 13.47, per 1000 atoms: 0.58 Number of scatterers: 23187 At special positions: 0 Unit cell: (136.53, 136.53, 152.52, 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 122 16.00 Mg 5 11.99 O 4082 8.00 N 3822 7.00 C 15156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 904 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 904 " distance=2.02 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 721 " distance=2.02 Simple disulfide: pdb=" SG CYS D 894 " - pdb=" SG CYS D 904 " distance=2.02 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: 9.59 Conformation dependent library (CDL) restraints added in 2.9 seconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 0 sheets defined 62.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.973A pdb=" N UNK A 11 " --> pdb=" O UNK A 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N UNK A 12 " --> pdb=" O UNK A 8 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N UNK A 13 " --> pdb=" O UNK A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 removed outlier: 3.936A pdb=" N UNK A 35 " --> pdb=" O UNK A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 306 through 312 Proline residue: A 310 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 312' Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.971A pdb=" N ILE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 486 through 504 removed outlier: 4.284A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 541 through 547 removed outlier: 4.315A pdb=" N LEU A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.540A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.646A pdb=" N HIS A 688 " --> pdb=" O TYR A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 713 removed outlier: 4.133A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 742 Processing helix chain 'A' and resid 753 through 757 Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.544A pdb=" N PHE A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 777 " --> pdb=" O PHE A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 818 removed outlier: 3.903A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 808 " --> pdb=" O CYS A 804 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 814 " --> pdb=" O TRP A 810 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 815 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 833 removed outlier: 4.253A pdb=" N GLY A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A 833 " --> pdb=" O MET A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 839 through 860 removed outlier: 4.194A pdb=" N ILE A 844 " --> pdb=" O TYR A 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 849 " --> pdb=" O MET A 845 " (cutoff:3.500A) Proline residue: A 855 - end of helix removed outlier: 4.002A pdb=" N ILE A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 879 removed outlier: 4.587A pdb=" N HIS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Proline residue: A 878 - end of helix Processing helix chain 'A' and resid 911 through 921 removed outlier: 3.506A pdb=" N ALA A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 932 No H-bonds generated for 'chain 'A' and resid 929 through 932' Processing helix chain 'A' and resid 939 through 952 removed outlier: 4.240A pdb=" N ILE A 944 " --> pdb=" O GLN A 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 957 No H-bonds generated for 'chain 'A' and resid 954 through 957' Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 1002 through 1025 removed outlier: 3.893A pdb=" N GLU A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1067 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.972A pdb=" N UNK B 11 " --> pdb=" O UNK B 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N UNK B 12 " --> pdb=" O UNK B 8 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 removed outlier: 3.936A pdb=" N UNK B 35 " --> pdb=" O UNK B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 306 through 312 Proline residue: B 310 - end of helix No H-bonds generated for 'chain 'B' and resid 306 through 312' Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 345 through 348 No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 460 through 469 removed outlier: 3.970A pdb=" N ILE B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 486 through 504 removed outlier: 4.284A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 521 through 524 No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 541 through 547 removed outlier: 4.315A pdb=" N LEU B 546 " --> pdb=" O MET B 542 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 586 Processing helix chain 'B' and resid 597 through 603 removed outlier: 3.770A pdb=" N SER B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 4.257A pdb=" N MET B 611 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 612 " --> pdb=" O ILE B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.646A pdb=" N HIS B 688 " --> pdb=" O TYR B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 713 removed outlier: 4.133A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 742 Processing helix chain 'B' and resid 753 through 757 Processing helix chain 'B' and resid 762 through 778 removed outlier: 3.544A pdb=" N PHE B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 777 " --> pdb=" O PHE B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 818 removed outlier: 3.902A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 807 " --> pdb=" O TYR B 803 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE B 808 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 810 " --> pdb=" O ASN B 806 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 815 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 816 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 833 removed outlier: 4.253A pdb=" N GLY B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 839 through 860 removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 849 " --> pdb=" O MET B 845 " (cutoff:3.500A) Proline residue: B 855 - end of helix removed outlier: 4.004A pdb=" N ILE B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 879 removed outlier: 4.587A pdb=" N HIS B 877 " --> pdb=" O ASP B 873 " (cutoff:3.500A) Proline residue: B 878 - end of helix Processing helix chain 'B' and resid 911 through 921 removed outlier: 3.507A pdb=" N ALA B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 920 " --> pdb=" O ALA B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 932 No H-bonds generated for 'chain 'B' and resid 929 through 932' Processing helix chain 'B' and resid 939 through 952 removed outlier: 4.240A pdb=" N ILE B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 957 No H-bonds generated for 'chain 'B' and resid 954 through 957' Processing helix chain 'B' and resid 971 through 973 No H-bonds generated for 'chain 'B' and resid 971 through 973' Processing helix chain 'B' and resid 1002 through 1025 removed outlier: 3.893A pdb=" N GLU B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP B1024 " --> pdb=" O PHE B1020 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP B1025 " --> pdb=" O ASP B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1067 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.973A pdb=" N UNK C 11 " --> pdb=" O UNK C 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N UNK C 12 " --> pdb=" O UNK C 8 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N UNK C 13 " --> pdb=" O UNK C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.936A pdb=" N UNK C 35 " --> pdb=" O UNK C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 54 through 63 Processing helix chain 'C' and resid 92 through 102 Processing helix chain 'C' and resid 105 through 108 No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 123 through 129 Proline residue: C 127 - end of helix No H-bonds generated for 'chain 'C' and resid 123 through 129' Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.971A pdb=" N ILE C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 303 through 321 removed outlier: 4.284A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 338 through 341 No H-bonds generated for 'chain 'C' and resid 338 through 341' Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 364 removed outlier: 4.315A pdb=" N LEU C 363 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.809A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.914A pdb=" N MET C 428 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 429 " --> pdb=" O ILE C 426 " (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 500 through 505 removed outlier: 3.646A pdb=" N HIS C 505 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 530 removed outlier: 4.132A pdb=" N LEU C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 559 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 579 through 595 removed outlier: 3.544A pdb=" N PHE C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 593 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 635 removed outlier: 3.903A pdb=" N ILE C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 625 " --> pdb=" O CYS C 621 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 631 " --> pdb=" O TRP C 627 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 650 removed outlier: 4.253A pdb=" N GLY C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS C 650 " --> pdb=" O MET C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 654 No H-bonds generated for 'chain 'C' and resid 652 through 654' Processing helix chain 'C' and resid 656 through 677 removed outlier: 4.194A pdb=" N ILE C 661 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 666 " --> pdb=" O MET C 662 " (cutoff:3.500A) Proline residue: C 672 - end of helix removed outlier: 4.003A pdb=" N ILE C 676 " --> pdb=" O PRO C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 4.586A pdb=" N HIS C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Proline residue: C 695 - end of helix Processing helix chain 'C' and resid 728 through 738 removed outlier: 3.506A pdb=" N ALA C 733 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 749 No H-bonds generated for 'chain 'C' and resid 746 through 749' Processing helix chain 'C' and resid 756 through 769 removed outlier: 4.240A pdb=" N ILE C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 774 No H-bonds generated for 'chain 'C' and resid 771 through 774' Processing helix chain 'C' and resid 788 through 790 No H-bonds generated for 'chain 'C' and resid 788 through 790' Processing helix chain 'C' and resid 819 through 842 removed outlier: 3.893A pdb=" N GLU C 834 " --> pdb=" O GLU C 830 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP C 842 " --> pdb=" O ASP C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 884 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.972A pdb=" N UNK D 11 " --> pdb=" O UNK D 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N UNK D 12 " --> pdb=" O UNK D 8 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N UNK D 13 " --> pdb=" O UNK D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 removed outlier: 3.936A pdb=" N UNK D 35 " --> pdb=" O UNK D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 290 No H-bonds generated for 'chain 'D' and resid 287 through 290' Processing helix chain 'D' and resid 306 through 312 Proline residue: D 310 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 312' Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 345 through 348 No H-bonds generated for 'chain 'D' and resid 345 through 348' Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.562A pdb=" N MET D 358 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 436 through 441 Processing helix chain 'D' and resid 460 through 469 removed outlier: 3.971A pdb=" N ILE D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 486 through 504 removed outlier: 4.284A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 516 No H-bonds generated for 'chain 'D' and resid 514 through 516' Processing helix chain 'D' and resid 521 through 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 528 through 537 Processing helix chain 'D' and resid 541 through 547 removed outlier: 4.315A pdb=" N LEU D 546 " --> pdb=" O MET D 542 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 547 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 586 Processing helix chain 'D' and resid 597 through 603 removed outlier: 3.802A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 612 removed outlier: 4.256A pdb=" N MET D 611 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 612 " --> pdb=" O ILE D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 622 No H-bonds generated for 'chain 'D' and resid 620 through 622' Processing helix chain 'D' and resid 683 through 688 removed outlier: 3.646A pdb=" N HIS D 688 " --> pdb=" O TYR D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 713 removed outlier: 4.132A pdb=" N LEU D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 742 Processing helix chain 'D' and resid 753 through 757 Processing helix chain 'D' and resid 762 through 778 removed outlier: 3.544A pdb=" N PHE D 773 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 818 removed outlier: 3.902A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 807 " --> pdb=" O TYR D 803 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE D 808 " --> pdb=" O CYS D 804 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 810 " --> pdb=" O ASN D 806 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 813 " --> pdb=" O PHE D 809 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 814 " --> pdb=" O TRP D 810 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 815 " --> pdb=" O TYR D 811 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 816 " --> pdb=" O VAL D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 833 removed outlier: 4.253A pdb=" N GLY D 832 " --> pdb=" O VAL D 828 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 839 through 860 removed outlier: 4.195A pdb=" N ILE D 844 " --> pdb=" O TYR D 840 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) Proline residue: D 855 - end of helix removed outlier: 4.003A pdb=" N ILE D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 879 removed outlier: 4.586A pdb=" N HIS D 877 " --> pdb=" O ASP D 873 " (cutoff:3.500A) Proline residue: D 878 - end of helix Processing helix chain 'D' and resid 911 through 921 removed outlier: 3.506A pdb=" N ALA D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE D 920 " --> pdb=" O ALA D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 932 No H-bonds generated for 'chain 'D' and resid 929 through 932' Processing helix chain 'D' and resid 939 through 952 removed outlier: 4.240A pdb=" N ILE D 944 " --> pdb=" O GLN D 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 957 No H-bonds generated for 'chain 'D' and resid 954 through 957' Processing helix chain 'D' and resid 971 through 973 No H-bonds generated for 'chain 'D' and resid 971 through 973' Processing helix chain 'D' and resid 1002 through 1025 removed outlier: 3.893A pdb=" N GLU D1017 " --> pdb=" O GLU D1013 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP D1025 " --> pdb=" O ASP D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1067 827 hydrogen bonds defined for protein. 2424 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: 6.85 Time building geometry restraints manager: 10.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3939 1.32 - 1.44: 6177 1.44 - 1.57: 13281 1.57 - 1.69: 36 1.69 - 1.81: 212 Bond restraints: 23645 Sorted by residual: bond pdb=" CAV Y01 C1303 " pdb=" CAZ Y01 C1303 " ideal model delta sigma weight residual 1.507 1.362 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CAV Y01 C1306 " pdb=" CAZ Y01 C1306 " ideal model delta sigma weight residual 1.507 1.378 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CAZ Y01 B1204 " pdb=" CBH Y01 B1204 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAZ Y01 A1203 " pdb=" CBH Y01 A1203 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CAV Y01 D1203 " pdb=" CAZ Y01 D1203 " ideal model delta sigma weight residual 1.507 1.390 0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 23640 not shown) Histogram of bond angle deviations from ideal: 93.74 - 103.15: 265 103.15 - 112.56: 12260 112.56 - 121.97: 15124 121.97 - 131.38: 4421 131.38 - 140.79: 159 Bond angle restraints: 32229 Sorted by residual: angle pdb=" C ILE C 167 " pdb=" N GLY C 168 " pdb=" CA GLY C 168 " ideal model delta sigma weight residual 121.41 140.79 -19.38 1.96e+00 2.60e-01 9.78e+01 angle pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta sigma weight residual 122.82 134.84 -12.02 1.42e+00 4.96e-01 7.16e+01 angle pdb=" C TRP B 480 " pdb=" N GLN B 481 " pdb=" CA GLN B 481 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 122.82 134.83 -12.01 1.42e+00 4.96e-01 7.15e+01 angle pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta sigma weight residual 122.82 134.82 -12.00 1.42e+00 4.96e-01 7.14e+01 ... (remaining 32224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 13309 26.92 - 53.84: 407 53.84 - 80.76: 26 80.76 - 107.68: 15 107.68 - 134.60: 6 Dihedral angle restraints: 13763 sinusoidal: 4651 harmonic: 9112 Sorted by residual: dihedral pdb=" CA TRP A 480 " pdb=" C TRP A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA TRP D 480 " pdb=" C TRP D 480 " pdb=" N GLN D 481 " pdb=" CA GLN D 481 " ideal model delta harmonic sigma weight residual 180.00 45.45 134.55 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA TRP C 297 " pdb=" C TRP C 297 " pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta harmonic sigma weight residual 180.00 45.47 134.53 0 5.00e+00 4.00e-02 7.24e+02 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3292 0.106 - 0.212: 334 0.212 - 0.318: 81 0.318 - 0.425: 43 0.425 - 0.531: 25 Chirality restraints: 3775 Sorted by residual: chirality pdb=" CBF Y01 A1206 " pdb=" CAS Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBH Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.45 -2.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CBG Y01 C1303 " pdb=" CAQ Y01 C1303 " pdb=" CBD Y01 C1303 " pdb=" CBI Y01 C1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CBG Y01 B1205 " pdb=" CAQ Y01 B1205 " pdb=" CBD Y01 B1205 " pdb=" CBI Y01 B1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 3772 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.033 2.00e-02 2.50e+03 6.63e-02 4.39e+01 pdb=" C ILE C 167 " 0.115 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY C 168 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 605 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO D 606 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 606 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 606 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 353 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C VAL A 353 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL A 353 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 354 " 0.023 2.00e-02 2.50e+03 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1276 2.71 - 3.44: 32449 3.44 - 4.17: 52054 4.17 - 4.90: 88325 Nonbonded interactions: 174105 Sorted by model distance: nonbonded pdb="MG MG D1201 " pdb=" O HOH D1307 " model vdw 1.254 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH B1301 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.047 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH C1404 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1201 " pdb=" O HOH D1303 " model vdw 2.079 2.170 ... (remaining 174100 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 346 or (resid 347 through 348 and (name N or nam \ e CA or name C or name O or name CB )) or resid 349 through 351 or (resid 352 an \ d (name N or name CA or name C or name O or name CB )) or resid 353 through 362 \ or (resid 363 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 432 or (resid 433 through 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 443 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 455 through 484 or (resi \ d 485 and (name N or name CA or name C or name O or name CB )) or resid 486 thro \ ugh 514 or (resid 515 through 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 538 or (resid 539 through 540 and (name N or nam \ e CA or name C or name O or name CB )) or resid 541 through 550 or (resid 551 an \ d (name N or name CA or name C or name O or name CB )) or resid 552 through 1068 \ or resid 1203)) selection = (chain 'B' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 346 or (resid 347 through 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 353 \ or (resid 354 through 355 and (name N or name CA or name C or name O or name CB \ )) or resid 356 through 362 or (resid 363 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 439 or (resid 440 and (name \ N or name CA or name C or name O or name CB )) or resid 441 through 443 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 455 thro \ ugh 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) o \ r resid 486 through 514 or (resid 515 through 516 and (name N or name CA or name \ C or name O or name CB )) or resid 517 through 522 or (resid 523 and (name N or \ name CA or name C or name O or name CB )) or resid 524 through 538 or (resid 53 \ 9 through 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 1068 or resid 1203)) selection = (chain 'C' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 163 or (resid 164 through 165 an \ d (name N or name CA or name C or name O or name CB )) or resid 166 through 170 \ or (resid 171 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 179 or (resid 180 through 182 and (name N or name CA or \ name C or name O or name CB )) or resid 183 through 232 or (resid 233 through 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 249 or (resid 250 through 251 and (name N or name CA or name C or name O or name \ CB )) or resid 252 through 256 or (resid 257 and (name N or name CA or name C o \ r name O or name CB )) or resid 258 through 300 or (resid 301 through 302 and (n \ ame N or name CA or name C or name O or name CB )) or resid 303 through 331 or ( \ resid 332 through 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 355 or (resid 356 through 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 through 885 or resid 130 \ 3)) selection = (chain 'D' and (resid 1 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 353 or (resid 354 through 355 an \ d (name N or name CA or name C or name O or name CB )) or resid 356 through 433 \ or (resid 434 and (name N or name CA or name C or name O or name CB )) or resid \ 435 through 439 or (resid 440 and (name N or name CA or name C or name O or name \ CB )) or resid 441 through 443 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 455 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 605 or (resid 606 an \ d (name N or name CA or name C or name O or name CB )) or resid 607 through 1068 \ or resid 1203)) } 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 Mg 5 5.21 5 S 122 5.16 5 C 15156 2.51 5 N 3822 2.21 5 O 4082 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: 0.810 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: 0.020 Extract box with map and model: 5.700 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.210 Process input model: 57.410 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.145 23645 Z= 0.724 Angle : 1.653 19.383 32229 Z= 0.858 Chirality : 0.092 0.531 3775 Planarity : 0.009 0.135 3968 Dihedral : 13.726 134.605 7791 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.33 % Twisted Proline : 3.70 % Twisted General : 3.75 % 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: -5.69 (0.12), residues: 2528 helix: -3.51 (0.09), residues: 1578 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 628 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 637 average time/residue: 0.3320 time to fit residues: 328.0193 Evaluate side-chains 419 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2154 time to fit residues: 4.1917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 279 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 578 GLN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1048 GLN B 395 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN B 578 GLN B 590 ASN B 806 ASN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 395 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN D 395 GLN ** D 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN D 538 GLN D 553 ASN D 578 GLN D 590 ASN D 763 ASN ** D 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1014 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 23645 Z= 0.374 Angle : 1.141 18.284 32229 Z= 0.509 Chirality : 0.050 0.271 3775 Planarity : 0.005 0.078 3968 Dihedral : 10.778 111.365 3506 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.73 % Favored : 89.40 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 2.78 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.14), residues: 2528 helix: -2.08 (0.11), residues: 1604 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 485 time to evaluate : 2.542 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 43 residues processed: 538 average time/residue: 0.3397 time to fit residues: 294.4264 Evaluate side-chains 458 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 415 time to evaluate : 3.485 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2180 time to fit residues: 21.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 0.7980 chunk 302 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN B 461 ASN B 481 GLN B 896 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN B1044 GLN B1048 GLN C 323 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 623 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 538 GLN D 763 ASN ** D 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN D1057 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 23645 Z= 0.336 Angle : 1.105 18.461 32229 Z= 0.487 Chirality : 0.050 0.259 3775 Planarity : 0.005 0.073 3968 Dihedral : 10.257 110.196 3506 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.56 % Favored : 88.69 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.51 % Twisted Proline : 3.70 % Twisted General : 0.69 % 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: -3.36 (0.16), residues: 2528 helix: -1.40 (0.12), residues: 1618 sheet: None (None), residues: 0 loop : -3.72 (0.19), residues: 910 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 434 time to evaluate : 2.637 Fit side-chains outliers start: 81 outliers final: 34 residues processed: 483 average time/residue: 0.3145 time to fit residues: 243.0071 Evaluate side-chains 431 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 397 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2168 time to fit residues: 17.3659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 297 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 266 optimal weight: 0.0470 chunk 80 optimal weight: 10.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 837 ASN A1014 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 590 ASN ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN B 961 HIS B1048 GLN C 355 GLN C 580 ASN C 623 ASN C 753 ASN C 831 GLN D 482 HIS ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN D 936 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 23645 Z= 0.198 Angle : 1.029 18.563 32229 Z= 0.445 Chirality : 0.045 0.224 3775 Planarity : 0.004 0.054 3968 Dihedral : 9.524 107.362 3506 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.02 % Favored : 90.31 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -2.80 (0.16), residues: 2528 helix: -0.89 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -3.64 (0.18), residues: 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 439 time to evaluate : 2.732 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 36 residues processed: 481 average time/residue: 0.3222 time to fit residues: 248.6345 Evaluate side-chains 428 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 392 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2253 time to fit residues: 18.4301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 267 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 763 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN A1014 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 590 ASN C 355 GLN C 580 ASN C 713 ASN C 778 HIS C 831 GLN ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN D 538 GLN D1014 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 23645 Z= 0.248 Angle : 1.041 18.466 32229 Z= 0.450 Chirality : 0.047 0.262 3775 Planarity : 0.004 0.051 3968 Dihedral : 9.390 108.913 3506 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.32 % Favored : 88.88 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.56 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.57 (0.17), residues: 2528 helix: -0.64 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -3.67 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 405 time to evaluate : 2.729 Fit side-chains outliers start: 55 outliers final: 31 residues processed: 436 average time/residue: 0.3253 time to fit residues: 227.9018 Evaluate side-chains 411 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 380 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2127 time to fit residues: 15.8216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0040 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 538 GLN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 806 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS C 298 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 23645 Z= 0.225 Angle : 1.023 18.569 32229 Z= 0.440 Chirality : 0.046 0.228 3775 Planarity : 0.004 0.051 3968 Dihedral : 9.143 108.091 3506 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.22 % Favored : 89.91 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.18 (0.17), residues: 2528 helix: -0.29 (0.14), residues: 1581 sheet: None (None), residues: 0 loop : -3.54 (0.18), residues: 947 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 405 time to evaluate : 2.623 Fit side-chains outliers start: 37 outliers final: 26 residues processed: 417 average time/residue: 0.3167 time to fit residues: 212.8590 Evaluate side-chains 414 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 388 time to evaluate : 2.746 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2304 time to fit residues: 13.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 166 optimal weight: 0.0050 chunk 296 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 538 GLN A 723 GLN A 763 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 355 GLN C 580 ASN D 538 GLN D1014 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 23645 Z= 0.191 Angle : 1.003 18.123 32229 Z= 0.429 Chirality : 0.045 0.291 3775 Planarity : 0.004 0.049 3968 Dihedral : 8.817 107.573 3506 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.49 % Favored : 89.64 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.84 (0.17), residues: 2528 helix: -0.07 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -3.35 (0.18), residues: 932 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 438 time to evaluate : 2.769 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 454 average time/residue: 0.3300 time to fit residues: 239.0784 Evaluate side-chains 415 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 403 time to evaluate : 2.667 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2534 time to fit residues: 8.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 89 optimal weight: 0.0070 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 806 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN C 580 ASN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 23645 Z= 0.205 Angle : 1.011 17.818 32229 Z= 0.433 Chirality : 0.045 0.229 3775 Planarity : 0.004 0.050 3968 Dihedral : 8.688 109.403 3506 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.14 % Favored : 89.99 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.72 (0.17), residues: 2528 helix: 0.02 (0.14), residues: 1598 sheet: None (None), residues: 0 loop : -3.29 (0.18), residues: 930 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 417 time to evaluate : 2.751 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 425 average time/residue: 0.3332 time to fit residues: 226.8123 Evaluate side-chains 418 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 407 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2221 time to fit residues: 7.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 261 optimal weight: 0.0030 chunk 275 optimal weight: 0.0030 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 522 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23645 Z= 0.203 Angle : 1.007 17.339 32229 Z= 0.430 Chirality : 0.045 0.225 3775 Planarity : 0.004 0.050 3968 Dihedral : 8.573 108.976 3506 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.61 % Favored : 89.60 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.61 (0.17), residues: 2528 helix: 0.12 (0.14), residues: 1593 sheet: None (None), residues: 0 loop : -3.25 (0.18), residues: 935 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 414 time to evaluate : 2.784 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 416 average time/residue: 0.3290 time to fit residues: 218.4626 Evaluate side-chains 416 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 405 time to evaluate : 2.528 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2058 time to fit residues: 7.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.5980 chunk 292 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 188 optimal weight: 0.0470 chunk 149 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 837 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23645 Z= 0.197 Angle : 1.009 17.040 32229 Z= 0.431 Chirality : 0.044 0.225 3775 Planarity : 0.004 0.050 3968 Dihedral : 8.421 108.834 3506 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.61 % Favored : 89.64 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.44 (0.17), residues: 2528 helix: 0.23 (0.14), residues: 1598 sheet: None (None), residues: 0 loop : -3.16 (0.18), residues: 930 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 421 time to evaluate : 2.491 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 425 average time/residue: 0.3158 time to fit residues: 217.4530 Evaluate side-chains 413 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 407 time to evaluate : 2.696 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2308 time to fit residues: 6.0912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 10.0000 chunk 260 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 251 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN B 461 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139742 restraints weight = 33595.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143072 restraints weight = 18424.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145093 restraints weight = 12743.593| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23645 Z= 0.199 Angle : 1.007 16.881 32229 Z= 0.431 Chirality : 0.044 0.260 3775 Planarity : 0.004 0.050 3968 Dihedral : 8.306 109.011 3506 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.05 % Favored : 89.24 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.60 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.33 (0.17), residues: 2528 helix: 0.30 (0.14), residues: 1595 sheet: None (None), residues: 0 loop : -3.05 (0.18), residues: 933 =============================================================================== Job complete usr+sys time: 4703.95 seconds wall clock time: 86 minutes 0.68 seconds (5160.68 seconds total)