Starting phenix.real_space_refine on Mon Dec 11 20:10:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/12_2023/7yks_33896.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 12308 2.51 5 N 3196 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 541": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 974": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1120": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 974": "NH1" <-> "NH2" Residue "B ARG 1042": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1140": "NH1" <-> "NH2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "C ARG 912": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1042": "NH1" <-> "NH2" Residue "C ARG 1120": "NH1" <-> "NH2" Residue "C ARG 1122": "NH1" <-> "NH2" Residue "C ARG 1130": "NH1" <-> "NH2" Residue "C ARG 1140": "NH1" <-> "NH2" Residue "D ARG 541": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "D ARG 912": "NH1" <-> "NH2" Residue "D ARG 974": "NH1" <-> "NH2" Residue "D ARG 1042": "NH1" <-> "NH2" Residue "D ARG 1120": "NH1" <-> "NH2" Residue "D ARG 1122": "NH1" <-> "NH2" Residue "D ARG 1130": "NH1" <-> "NH2" Residue "D ARG 1140": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18984 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.54, per 1000 atoms: 0.50 Number of scatterers: 18984 At special positions: 0 Unit cell: (112.11, 112.11, 145.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3344 8.00 N 3196 7.00 C 12308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 3.1 seconds 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 70.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE A 561 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL A 597 " --> pdb=" O HIS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 842 removed outlier: 3.661A pdb=" N ILE A 835 " --> pdb=" O CYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 876 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER A 964 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 965 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 966 " --> pdb=" O LEU A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 966' Processing helix chain 'A' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 989 through 995 Processing helix chain 'A' and resid 1000 through 1015 removed outlier: 3.544A pdb=" N LEU A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1050 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A1055 " --> pdb=" O THR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A1063 " --> pdb=" O HIS A1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A1065 " --> pdb=" O TRP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU A1138 " --> pdb=" O GLN A1134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1143 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.503A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE B 561 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL B 597 " --> pdb=" O HIS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.528A pdb=" N THR B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE B 835 " --> pdb=" O CYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 876 Processing helix chain 'B' and resid 877 through 881 Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR B 892 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG B 912 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 913 " --> pdb=" O LEU B 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 909 through 913' Processing helix chain 'B' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER B 964 " --> pdb=" O ASN B 961 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 965 " --> pdb=" O HIS B 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 966 " --> pdb=" O LEU B 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 966' Processing helix chain 'B' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 989 through 995 Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU B1006 " --> pdb=" O MET B1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B1036 " --> pdb=" O GLU B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B1050 " --> pdb=" O GLN B1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU B1062 " --> pdb=" O PRO B1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B1063 " --> pdb=" O HIS B1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B1065 " --> pdb=" O TRP B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1117 through 1146 removed outlier: 3.632A pdb=" N LEU B1138 " --> pdb=" O GLN B1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B1144 " --> pdb=" O ARG B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE C 561 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL C 597 " --> pdb=" O HIS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 621 Processing helix chain 'C' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 726 removed outlier: 3.529A pdb=" N THR C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 763 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE C 835 " --> pdb=" O CYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 876 Processing helix chain 'C' and resid 877 through 881 Processing helix chain 'C' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 913 removed outlier: 3.742A pdb=" N ARG C 912 " --> pdb=" O PHE C 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 913' Processing helix chain 'C' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 removed outlier: 3.750A pdb=" N SER C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER C 964 " --> pdb=" O ASN C 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 965 " --> pdb=" O HIS C 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 966 " --> pdb=" O LEU C 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 961 through 966' Processing helix chain 'C' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 989 through 995 Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU C1006 " --> pdb=" O MET C1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY C1029 " --> pdb=" O GLY C1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C1036 " --> pdb=" O GLU C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C1050 " --> pdb=" O GLN C1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C1055 " --> pdb=" O THR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU C1062 " --> pdb=" O PRO C1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C1063 " --> pdb=" O HIS C1059 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C1064 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C1065 " --> pdb=" O TRP C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU C1138 " --> pdb=" O GLN C1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1143 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C1144 " --> pdb=" O ARG C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG D 486 " --> pdb=" O HIS D 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE D 561 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 566 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 removed outlier: 3.824A pdb=" N VAL D 597 " --> pdb=" O HIS D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 Processing helix chain 'D' and resid 623 through 632 removed outlier: 3.789A pdb=" N ALA D 629 " --> pdb=" O GLU D 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.043A pdb=" N ILE D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 746 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 777 removed outlier: 4.252A pdb=" N ASN D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 765 " --> pdb=" O SER D 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE D 835 " --> pdb=" O CYS D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 852 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 876 Processing helix chain 'D' and resid 877 through 881 Processing helix chain 'D' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG D 912 " --> pdb=" O PHE D 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 913 " --> pdb=" O LEU D 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 909 through 913' Processing helix chain 'D' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 932 " --> pdb=" O GLN D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER D 964 " --> pdb=" O ASN D 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 965 " --> pdb=" O HIS D 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 966 " --> pdb=" O LEU D 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 961 through 966' Processing helix chain 'D' and resid 967 through 978 removed outlier: 3.588A pdb=" N LEU D 973 " --> pdb=" O PRO D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 989 through 995 Processing helix chain 'D' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY D1029 " --> pdb=" O GLY D1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D1036 " --> pdb=" O GLU D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1055 removed outlier: 4.065A pdb=" N LEU D1043 " --> pdb=" O GLN D1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS D1050 " --> pdb=" O GLN D1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D1055 " --> pdb=" O THR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU D1062 " --> pdb=" O PRO D1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1063 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D1064 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D1065 " --> pdb=" O TRP D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU D1138 " --> pdb=" O GLN D1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 673 Processing sheet with id=AA2, first strand: chain 'A' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU A 820 " --> pdb=" O ILE A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 673 Processing sheet with id=AA4, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU B 820 " --> pdb=" O ILE B 887 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 671 through 673 Processing sheet with id=AA6, first strand: chain 'C' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU C 820 " --> pdb=" O ILE C 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 671 through 673 Processing sheet with id=AA8, first strand: chain 'D' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU D 820 " --> pdb=" O ILE D 887 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2688 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: 5.55 Time building geometry restraints manager: 6.83 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: 5565 1.33 - 1.45: 2783 1.45 - 1.57: 10776 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 19372 Sorted by residual: bond pdb=" CA GLU B 982 " pdb=" CB GLU B 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.30e+01 bond pdb=" CA GLU C 982 " pdb=" CB GLU C 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.30e+01 bond pdb=" CA GLU A 982 " pdb=" CB GLU A 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.28e+01 bond pdb=" CA GLU D 982 " pdb=" CB GLU D 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.28e+01 bond pdb=" CB ARG B1140 " pdb=" CG ARG B1140 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.46e+00 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 396 105.66 - 112.74: 10263 112.74 - 119.82: 7053 119.82 - 126.90: 8319 126.90 - 133.98: 213 Bond angle restraints: 26244 Sorted by residual: angle pdb=" N PRO D1074 " pdb=" CA PRO D1074 " pdb=" CB PRO D1074 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.57e+01 angle pdb=" N PRO B1074 " pdb=" CA PRO B1074 " pdb=" CB PRO B1074 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N PRO C1074 " pdb=" CA PRO C1074 " pdb=" CB PRO C1074 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N PRO A1074 " pdb=" CA PRO A1074 " pdb=" CB PRO A1074 " ideal model delta sigma weight residual 103.00 110.38 -7.38 1.10e+00 8.26e-01 4.51e+01 angle pdb=" C LEU C 610 " pdb=" N ASP C 611 " pdb=" CA ASP C 611 " ideal model delta sigma weight residual 122.46 130.04 -7.58 1.41e+00 5.03e-01 2.89e+01 ... (remaining 26239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 10992 14.81 - 29.62: 543 29.62 - 44.43: 177 44.43 - 59.23: 4 59.23 - 74.04: 8 Dihedral angle restraints: 11724 sinusoidal: 4700 harmonic: 7024 Sorted by residual: dihedral pdb=" CA PHE A 937 " pdb=" C PHE A 937 " pdb=" N SER A 938 " pdb=" CA SER A 938 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE B 937 " pdb=" C PHE B 937 " pdb=" N SER B 938 " pdb=" CA SER B 938 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 937 " pdb=" C PHE D 937 " pdb=" N SER D 938 " pdb=" CA SER D 938 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 11721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1938 0.050 - 0.100: 885 0.100 - 0.150: 202 0.150 - 0.200: 35 0.200 - 0.250: 28 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA PRO D1074 " pdb=" N PRO D1074 " pdb=" C PRO D1074 " pdb=" CB PRO D1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO A1074 " pdb=" N PRO A1074 " pdb=" C PRO A1074 " pdb=" CB PRO A1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C1074 " pdb=" N PRO C1074 " pdb=" C PRO C1074 " pdb=" CB PRO C1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 3085 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 547 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO B 548 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 547 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO C 548 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 548 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 548 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 547 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 548 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " 0.036 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5518 2.81 - 3.33: 16374 3.33 - 3.86: 29532 3.86 - 4.38: 36420 4.38 - 4.90: 61899 Nonbonded interactions: 149743 Sorted by model distance: nonbonded pdb=" OH TYR B 748 " pdb=" OE2 GLU B1054 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR A 748 " pdb=" OE2 GLU A1054 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR C 748 " pdb=" OE2 GLU C1054 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR D 748 " pdb=" OE2 GLU D1054 " model vdw 2.292 2.440 nonbonded pdb=" O GLN A 523 " pdb=" NH2 ARG B1140 " model vdw 2.325 2.520 ... (remaining 149738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.920 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: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.180 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1101 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 : 0.008 0.093 19372 Z= 0.504 Angle : 0.995 11.164 26244 Z= 0.515 Chirality : 0.061 0.250 3088 Planarity : 0.007 0.065 3256 Dihedral : 10.268 74.042 7156 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.58 (0.10), residues: 2332 helix: -4.65 (0.05), residues: 1568 sheet: -2.11 (0.81), residues: 40 loop : -3.17 (0.18), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 867 HIS 0.008 0.002 HIS D 518 PHE 0.033 0.003 PHE A 948 TYR 0.028 0.003 TYR B 623 ARG 0.014 0.001 ARG D1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 257 average time/residue: 1.1901 time to fit residues: 347.3156 Evaluate side-chains 190 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.0809 time to fit residues: 4.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 9.9990 chunk 178 optimal weight: 0.0670 chunk 99 optimal weight: 0.1980 chunk 61 optimal weight: 0.3980 chunk 120 optimal weight: 0.0170 chunk 95 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 214 optimal weight: 0.0670 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 726 HIS A 742 GLN A 753 HIS A 842 ASN A 882 GLN A 967 ASN A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 HIS B 491 ASN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 738 GLN B 746 ASN B 842 ASN B 888 ASN B 967 ASN B 991 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN C 568 HIS C 570 HIS C 721 ASN C 742 GLN C 753 HIS ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 ASN ** C 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN D 742 GLN D 753 HIS ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 ASN D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1492 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19372 Z= 0.160 Angle : 0.624 8.400 26244 Z= 0.325 Chirality : 0.041 0.155 3088 Planarity : 0.005 0.052 3256 Dihedral : 5.104 25.406 2568 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.90 % Allowed : 9.13 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.14), residues: 2332 helix: -2.65 (0.10), residues: 1636 sheet: -2.72 (0.80), residues: 40 loop : -2.39 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1061 HIS 0.008 0.001 HIS A 568 PHE 0.015 0.001 PHE D 948 TYR 0.011 0.001 TYR B 617 ARG 0.005 0.000 ARG B 845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 9 residues processed: 223 average time/residue: 1.1797 time to fit residues: 300.8087 Evaluate side-chains 183 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.6905 time to fit residues: 8.0213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 746 ASN ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 721 ASN B 962 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 726 HIS C 738 GLN ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3277 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 19372 Z= 0.322 Angle : 0.808 12.462 26244 Z= 0.414 Chirality : 0.047 0.204 3088 Planarity : 0.006 0.060 3256 Dihedral : 5.112 26.683 2568 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.80 % Allowed : 10.46 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2332 helix: -1.40 (0.12), residues: 1600 sheet: -2.58 (0.81), residues: 40 loop : -2.40 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 903 HIS 0.011 0.002 HIS D 584 PHE 0.027 0.003 PHE C 937 TYR 0.037 0.002 TYR A 993 ARG 0.007 0.001 ARG D 821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 10 residues processed: 273 average time/residue: 1.1086 time to fit residues: 348.5351 Evaluate side-chains 201 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 1.3122 time to fit residues: 10.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 8.9990 chunk 161 optimal weight: 0.0670 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS B 753 HIS B1021 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS B1144 GLN C 482 HIS C 518 HIS ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1121 GLN C1135 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS D 550 GLN D 721 ASN ** D 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 959 GLN D1063 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4123 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19372 Z= 0.226 Angle : 0.678 13.270 26244 Z= 0.338 Chirality : 0.042 0.198 3088 Planarity : 0.004 0.064 3256 Dihedral : 4.560 23.249 2568 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.23 % Allowed : 13.45 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2332 helix: -0.66 (0.13), residues: 1592 sheet: -2.41 (0.80), residues: 40 loop : -2.09 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 903 HIS 0.018 0.001 HIS B 584 PHE 0.027 0.002 PHE D 752 TYR 0.016 0.001 TYR D 623 ARG 0.006 0.001 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 227 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 9 residues processed: 250 average time/residue: 1.0599 time to fit residues: 305.6251 Evaluate side-chains 201 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.7057 time to fit residues: 4.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 753 HIS A 777 ASN A 911 GLN A 962 HIS A 991 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 842 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 HIS C 967 ASN ** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 1.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 19372 Z= 0.287 Angle : 0.798 14.345 26244 Z= 0.399 Chirality : 0.046 0.201 3088 Planarity : 0.006 0.091 3256 Dihedral : 4.909 27.984 2568 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.42 % Allowed : 14.59 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2332 helix: -0.47 (0.13), residues: 1608 sheet: -2.37 (0.80), residues: 40 loop : -2.08 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 745 HIS 0.012 0.002 HIS C 891 PHE 0.020 0.002 PHE D 691 TYR 0.026 0.002 TYR C 557 ARG 0.011 0.001 ARG B 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 276 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 12 residues processed: 313 average time/residue: 1.2217 time to fit residues: 434.7462 Evaluate side-chains 209 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.7548 time to fit residues: 8.5479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 0.0670 chunk 189 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS A 777 ASN A 911 GLN A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS B 842 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 HIS D 738 GLN D 753 HIS D 777 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 1.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19372 Z= 0.154 Angle : 0.621 11.777 26244 Z= 0.310 Chirality : 0.040 0.155 3088 Planarity : 0.004 0.090 3256 Dihedral : 4.257 24.135 2568 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.95 % Allowed : 18.11 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2332 helix: 0.04 (0.14), residues: 1624 sheet: -2.33 (0.79), residues: 40 loop : -2.13 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 745 HIS 0.020 0.001 HIS B 648 PHE 0.011 0.001 PHE D 923 TYR 0.022 0.001 TYR C 870 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 12 residues processed: 254 average time/residue: 1.1537 time to fit residues: 335.0322 Evaluate side-chains 209 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.3694 time to fit residues: 5.9319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS A 753 HIS ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 GLN C 753 HIS ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 1.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 19372 Z= 0.253 Angle : 0.759 19.192 26244 Z= 0.380 Chirality : 0.044 0.212 3088 Planarity : 0.005 0.087 3256 Dihedral : 4.588 23.172 2568 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.61 % Allowed : 18.01 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2332 helix: 0.02 (0.13), residues: 1632 sheet: -2.17 (0.81), residues: 40 loop : -2.19 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 903 HIS 0.017 0.001 HIS B 648 PHE 0.027 0.002 PHE A 909 TYR 0.037 0.002 TYR C 621 ARG 0.012 0.001 ARG D1122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 315 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 18 residues processed: 354 average time/residue: 1.1887 time to fit residues: 477.9481 Evaluate side-chains 256 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 4 average time/residue: 0.8024 time to fit residues: 6.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS A 648 HIS A 863 ASN A1046 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS C 721 ASN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN D 742 GLN D 753 HIS D1050 HIS ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 1.9531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 19372 Z= 0.435 Angle : 0.950 14.493 26244 Z= 0.482 Chirality : 0.052 0.354 3088 Planarity : 0.007 0.085 3256 Dihedral : 5.418 27.187 2568 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.76 % Allowed : 20.34 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2332 helix: -0.62 (0.12), residues: 1630 sheet: -1.86 (0.85), residues: 40 loop : -2.67 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 867 HIS 0.016 0.002 HIS B 543 PHE 0.032 0.003 PHE A 483 TYR 0.066 0.003 TYR B 621 ARG 0.013 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 457 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 13 residues processed: 491 average time/residue: 1.2593 time to fit residues: 696.6142 Evaluate side-chains 322 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 309 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1779 time to fit residues: 2.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 0.0970 chunk 139 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS C 823 ASN C1046 GLN ** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN D 525 HIS D 721 ASN D 742 GLN D 753 HIS D 991 ASN ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 2.0032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19372 Z= 0.225 Angle : 0.694 12.227 26244 Z= 0.353 Chirality : 0.043 0.187 3088 Planarity : 0.005 0.063 3256 Dihedral : 4.650 21.027 2568 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.38 % Allowed : 25.00 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2332 helix: -0.03 (0.13), residues: 1612 sheet: -1.66 (0.87), residues: 40 loop : -2.29 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 903 HIS 0.012 0.001 HIS B 648 PHE 0.023 0.002 PHE B 683 TYR 0.031 0.002 TYR D 623 ARG 0.011 0.001 ARG A1140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 354 time to evaluate : 2.168 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 391 average time/residue: 1.1627 time to fit residues: 517.6860 Evaluate side-chains 314 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 296 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.2135 time to fit residues: 3.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 0.0070 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 540 HIS B 565 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 HIS ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 2.0389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19372 Z= 0.199 Angle : 0.651 12.080 26244 Z= 0.329 Chirality : 0.042 0.196 3088 Planarity : 0.004 0.067 3256 Dihedral : 4.329 19.806 2568 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.57 % Allowed : 27.23 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2332 helix: 0.29 (0.13), residues: 1608 sheet: -1.55 (0.89), residues: 40 loop : -2.09 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 903 HIS 0.010 0.001 HIS A 648 PHE 0.034 0.001 PHE A 909 TYR 0.032 0.002 TYR D 623 ARG 0.012 0.001 ARG B 912 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 2.114 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 351 average time/residue: 1.2092 time to fit residues: 486.3399 Evaluate side-chains 303 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 289 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.2172 time to fit residues: 3.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.8980 chunk 172 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 GLN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 HIS ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.172667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123304 restraints weight = 21318.600| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.45 r_work: 0.3098 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 2.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19372 Z= 0.194 Angle : 0.658 12.399 26244 Z= 0.329 Chirality : 0.042 0.242 3088 Planarity : 0.004 0.063 3256 Dihedral : 4.180 19.063 2568 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.14 % Allowed : 28.23 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2332 helix: 0.52 (0.13), residues: 1600 sheet: -1.54 (0.89), residues: 40 loop : -2.08 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 903 HIS 0.011 0.001 HIS A 648 PHE 0.018 0.001 PHE B 504 TYR 0.027 0.001 TYR D 623 ARG 0.009 0.001 ARG B 912 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6990.95 seconds wall clock time: 128 minutes 38.68 seconds (7718.68 seconds total)