Starting phenix.real_space_refine on Sun Mar 17 21:24:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/03_2024/7yks_33896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/03_2024/7yks_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_33896/03_2024/7yks_33896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/03_2024/7yks_33896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/03_2024/7yks_33896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/03_2024/7yks_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.67, per 1000 atoms: 0.51 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: 7.54 Conformation dependent library (CDL) restraints added in 3.8 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: 2.21 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: 5.91 Time building geometry restraints manager: 8.17 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 51.290 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.120 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.770 ------------------------------------------------------------------------------- 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 : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 LEU cc_start: 0.6134 (mm) cc_final: 0.5904 (tm) REVERT: B 606 VAL cc_start: 0.3908 (m) cc_final: 0.3625 (p) REVERT: B 655 LEU cc_start: 0.2730 (mt) cc_final: 0.2430 (mt) REVERT: C 580 ASN cc_start: 0.2991 (m-40) cc_final: 0.2787 (t0) REVERT: D 726 HIS cc_start: 0.3912 (m-70) cc_final: 0.1837 (m170) REVERT: D 1061 TRP cc_start: 0.3381 (t-100) cc_final: 0.3011 (t60) outliers start: 0 outliers final: 2 residues processed: 257 average time/residue: 1.2368 time to fit residues: 358.7945 Evaluate side-chains 192 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain D residue 675 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 726 HIS 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: 0.1485 moved from start: 0.2547 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= 0.161 Angle : 0.621 8.258 26244 Z= 0.323 Chirality : 0.041 0.156 3088 Planarity : 0.005 0.051 3256 Dihedral : 5.268 38.926 2573 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.85 % Allowed : 8.98 % Favored : 89.16 % 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: -4.09 (0.14), residues: 2332 helix: -2.61 (0.10), residues: 1636 sheet: -2.73 (0.80), residues: 40 loop : -2.38 (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 0.012 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 245 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 206 time to evaluate : 2.000 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: A 630 MET cc_start: 0.2390 (mpp) cc_final: -0.0086 (ptm) REVERT: A 691 PHE cc_start: 0.3423 (OUTLIER) cc_final: 0.3110 (t80) REVERT: A 842 ASN cc_start: 0.4819 (OUTLIER) cc_final: 0.4608 (t0) REVERT: A 993 TYR cc_start: 0.5082 (t80) cc_final: 0.3916 (t80) REVERT: A 1131 MET cc_start: 0.2113 (OUTLIER) cc_final: 0.0090 (mmm) REVERT: B 606 VAL cc_start: 0.3844 (m) cc_final: 0.3538 (p) REVERT: B 970 MET cc_start: 0.0411 (tpt) cc_final: -0.0541 (mpm) REVERT: B 1012 MET cc_start: 0.1871 (OUTLIER) cc_final: 0.1498 (tpp) REVERT: B 1146 MET cc_start: 0.1107 (ptt) cc_final: -0.0712 (tmt) REVERT: C 554 MET cc_start: 0.1113 (mtt) cc_final: -0.0829 (tpt) REVERT: C 609 VAL cc_start: 0.6320 (t) cc_final: 0.5994 (p) REVERT: C 970 MET cc_start: 0.2824 (mmp) cc_final: -0.0453 (ttp) REVERT: C 1015 MET cc_start: 0.1798 (tpt) cc_final: 0.0732 (tpp) REVERT: D 726 HIS cc_start: 0.2974 (m90) cc_final: 0.1610 (m170) REVERT: D 922 MET cc_start: 0.2215 (mmt) cc_final: 0.1597 (mmt) REVERT: D 978 MET cc_start: -0.1325 (ppp) cc_final: -0.2341 (mpp) REVERT: D 1061 TRP cc_start: 0.3433 (t-100) cc_final: 0.3082 (t60) outliers start: 39 outliers final: 10 residues processed: 222 average time/residue: 1.1956 time to fit residues: 302.2293 Evaluate side-chains 189 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 992 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 178 optimal weight: 0.0870 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 842 ASN A 911 GLN A 962 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN B 482 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 721 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 ASN C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2384 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 19372 Z= 0.206 Angle : 0.648 11.420 26244 Z= 0.337 Chirality : 0.041 0.181 3088 Planarity : 0.005 0.054 3256 Dihedral : 4.780 39.743 2571 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.38 % Allowed : 10.79 % Favored : 86.83 % 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: -2.50 (0.16), residues: 2332 helix: -1.19 (0.12), residues: 1600 sheet: -2.56 (0.82), residues: 40 loop : -2.39 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1061 HIS 0.035 0.001 HIS C 570 PHE 0.017 0.002 PHE B 985 TYR 0.019 0.001 TYR D 687 ARG 0.004 0.000 ARG B 845 *********************** 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 259 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.2878 (pp-130) cc_final: 0.2478 (pp-130) REVERT: A 842 ASN cc_start: 0.5211 (OUTLIER) cc_final: 0.4661 (t0) REVERT: A 993 TYR cc_start: 0.5998 (t80) cc_final: 0.5207 (OUTLIER) REVERT: A 1131 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.0407 (mmm) REVERT: C 1045 MET cc_start: 0.3600 (tpp) cc_final: 0.3138 (ptt) REVERT: C 1131 MET cc_start: 0.1311 (OUTLIER) cc_final: -0.0508 (ptt) REVERT: D 978 MET cc_start: 0.0108 (OUTLIER) cc_final: -0.1069 (pp-130) REVERT: D 1020 MET cc_start: 0.3507 (mmm) cc_final: 0.2581 (ppp) outliers start: 50 outliers final: 13 residues processed: 231 average time/residue: 1.1490 time to fit residues: 303.9252 Evaluate side-chains 192 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 978 MET Chi-restraints excluded: chain D residue 992 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 746 ASN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 518 HIS ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 842 ASN ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 HIS B1135 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS C 742 GLN C 753 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 ASN D1050 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 0.9685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 19372 Z= 0.381 Angle : 0.947 21.816 26244 Z= 0.475 Chirality : 0.051 0.357 3088 Planarity : 0.007 0.101 3256 Dihedral : 5.677 44.076 2571 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 3.56 % Allowed : 11.36 % Favored : 85.08 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.30 (0.16), residues: 2332 helix: -1.00 (0.12), residues: 1612 sheet: -2.56 (0.78), residues: 40 loop : -2.46 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B1061 HIS 0.044 0.003 HIS C 565 PHE 0.054 0.003 PHE A 965 TYR 0.034 0.003 TYR B 617 ARG 0.014 0.001 ARG B 636 *********************** 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 348 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 2.341 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: A 615 ILE cc_start: 0.4475 (OUTLIER) cc_final: 0.4143 (mt) REVERT: A 845 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7043 (tmm160) REVERT: A 1131 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5473 (tpt) REVERT: B 612 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5582 (tmm) REVERT: B 630 MET cc_start: 0.3141 (mmp) cc_final: 0.0625 (ptm) REVERT: C 500 GLU cc_start: 0.3407 (tp30) cc_final: 0.2746 (mm-30) REVERT: C 1131 MET cc_start: 0.3468 (OUTLIER) cc_final: 0.3190 (tpt) REVERT: D 743 MET cc_start: 0.5334 (ppp) cc_final: 0.5073 (ppp) REVERT: D 844 MET cc_start: 0.4337 (OUTLIER) cc_final: 0.4059 (tpt) REVERT: D 1037 ASN cc_start: 0.5484 (m-40) cc_final: 0.5076 (m-40) outliers start: 75 outliers final: 16 residues processed: 307 average time/residue: 1.1152 time to fit residues: 391.4974 Evaluate side-chains 218 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 912 ARG Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 1020 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 988 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 777 ASN A 961 ASN A 991 ASN A1121 GLN B 568 HIS ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 962 HIS C 518 HIS C 721 ASN ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN C1136 HIS ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS D 721 ASN D1021 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 1.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19372 Z= 0.234 Angle : 0.690 11.023 26244 Z= 0.349 Chirality : 0.043 0.301 3088 Planarity : 0.005 0.063 3256 Dihedral : 4.794 42.560 2571 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 14.92 % Favored : 82.75 % 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: -1.58 (0.17), residues: 2332 helix: -0.47 (0.13), residues: 1620 sheet: -2.41 (0.64), residues: 60 loop : -2.11 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 867 HIS 0.015 0.001 HIS B 648 PHE 0.020 0.002 PHE D 752 TYR 0.013 0.001 TYR C 760 ARG 0.014 0.001 ARG C 912 *********************** 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 300 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 956 ILE cc_start: 0.5710 (OUTLIER) cc_final: 0.4839 (mt) REVERT: B 910 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6968 (mp) REVERT: B 1002 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5511 (ppp) REVERT: C 630 MET cc_start: 0.2553 (tpp) cc_final: 0.1610 (ttt) REVERT: C 743 MET cc_start: 0.5732 (tmm) cc_final: 0.5493 (tmt) REVERT: C 1015 MET cc_start: 0.8348 (tpt) cc_final: 0.7933 (tpt) REVERT: C 1045 MET cc_start: 0.5165 (tpp) cc_final: 0.4736 (tpt) REVERT: D 560 THR cc_start: 0.3351 (t) cc_final: 0.2902 (m) REVERT: D 743 MET cc_start: 0.5994 (ppp) cc_final: 0.5733 (ppp) REVERT: D 986 VAL cc_start: 0.8464 (m) cc_final: 0.8220 (t) outliers start: 49 outliers final: 11 residues processed: 274 average time/residue: 1.2080 time to fit residues: 374.9347 Evaluate side-chains 208 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 876 MET Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 1030 ASP Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 189 optimal weight: 0.3980 chunk 105 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 A 776 ASN B 593 HIS ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 1.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19372 Z= 0.198 Angle : 0.658 11.453 26244 Z= 0.331 Chirality : 0.042 0.170 3088 Planarity : 0.004 0.054 3256 Dihedral : 4.404 23.495 2568 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.66 % Allowed : 16.49 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2332 helix: -0.11 (0.13), residues: 1636 sheet: -2.35 (0.75), residues: 40 loop : -2.03 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 745 HIS 0.022 0.001 HIS B 753 PHE 0.022 0.002 PHE A 909 TYR 0.026 0.002 TYR B 490 ARG 0.013 0.001 ARG C1123 *********************** 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 354 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 298 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.5111 (t80) cc_final: 0.4310 (t80) REVERT: A 956 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5310 (mp) REVERT: B 778 ILE cc_start: 0.7832 (mm) cc_final: 0.7304 (mm) REVERT: B 1009 SER cc_start: 0.8533 (t) cc_final: 0.8238 (m) REVERT: C 630 MET cc_start: 0.2759 (tpp) cc_final: 0.2480 (ttt) REVERT: C 986 VAL cc_start: 0.9055 (m) cc_final: 0.8827 (t) REVERT: D 560 THR cc_start: 0.3772 (t) cc_final: 0.3333 (m) REVERT: D 931 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7898 (tp) REVERT: D 1140 ARG cc_start: 0.6756 (ttt180) cc_final: 0.6050 (ttt180) outliers start: 56 outliers final: 18 residues processed: 328 average time/residue: 1.2477 time to fit residues: 460.8787 Evaluate side-chains 255 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 820 GLU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 1030 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 931 ILE 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: 0.7980 chunk 130 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 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 A1144 GLN B 540 HIS B 648 HIS B 911 GLN C 482 HIS ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN C1121 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 HIS D 648 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 1.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19372 Z= 0.252 Angle : 0.807 15.360 26244 Z= 0.405 Chirality : 0.045 0.225 3088 Planarity : 0.005 0.060 3256 Dihedral : 4.666 31.578 2568 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 2.76 % Allowed : 18.49 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.35 (0.17), residues: 2332 helix: -0.24 (0.13), residues: 1660 sheet: -1.80 (0.83), residues: 40 loop : -2.37 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 903 HIS 0.013 0.002 HIS B 584 PHE 0.025 0.002 PHE C 900 TYR 0.065 0.002 TYR A 621 ARG 0.013 0.001 ARG B 912 *********************** 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 425 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 367 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: A 612 MET cc_start: 0.6602 (ptm) cc_final: 0.6144 (ptp) REVERT: A 671 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6143 (pt) REVERT: A 774 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8398 (ttt) REVERT: A 956 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6219 (mt) REVERT: B 519 ILE cc_start: 0.6245 (tt) cc_final: 0.5990 (tp) REVERT: B 580 ASN cc_start: 0.6796 (m-40) cc_final: 0.6173 (m-40) REVERT: B 621 TYR cc_start: 0.5855 (m-10) cc_final: 0.5447 (m-10) REVERT: B 688 SER cc_start: 0.8065 (p) cc_final: 0.7807 (t) REVERT: B 868 VAL cc_start: 0.8515 (p) cc_final: 0.8139 (m) REVERT: C 514 MET cc_start: 0.2775 (mmm) cc_final: 0.0623 (ptm) REVERT: C 659 MET cc_start: 0.4800 (OUTLIER) cc_final: 0.4561 (ppp) REVERT: D 560 THR cc_start: 0.5598 (t) cc_final: 0.5174 (m) REVERT: D 772 SER cc_start: 0.8017 (m) cc_final: 0.7570 (t) outliers start: 58 outliers final: 15 residues processed: 393 average time/residue: 1.2019 time to fit residues: 533.4440 Evaluate side-chains 285 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 266 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 914 ASP Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.0270 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A1046 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 753 HIS B1136 HIS ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN ** D 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 1.8133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 19372 Z= 0.288 Angle : 0.788 28.502 26244 Z= 0.389 Chirality : 0.047 0.518 3088 Planarity : 0.005 0.060 3256 Dihedral : 4.655 23.051 2568 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 2.42 % Allowed : 22.15 % Favored : 75.43 % 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: -1.09 (0.17), residues: 2332 helix: 0.01 (0.13), residues: 1612 sheet: -1.87 (0.87), residues: 40 loop : -2.30 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 867 HIS 0.011 0.001 HIS B 584 PHE 0.023 0.002 PHE D 691 TYR 0.040 0.002 TYR B1073 ARG 0.009 0.001 ARG B1122 *********************** 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 407 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 356 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 TYR cc_start: 0.7622 (m-10) cc_final: 0.7390 (m-10) REVERT: A 774 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8354 (ttt) REVERT: A 841 LEU cc_start: 0.7662 (tm) cc_final: 0.7368 (tp) REVERT: A 847 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.6943 (tp) REVERT: A 849 GLN cc_start: 0.7122 (tp40) cc_final: 0.6597 (tm-30) REVERT: A 913 PHE cc_start: 0.8835 (m-80) cc_final: 0.8616 (m-80) REVERT: A 956 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6756 (mt) REVERT: A 1020 MET cc_start: 0.8496 (mmm) cc_final: 0.8294 (mmp) REVERT: B 519 ILE cc_start: 0.7123 (tt) cc_final: 0.6875 (tp) REVERT: B 686 LYS cc_start: 0.7110 (mtpp) cc_final: 0.6835 (mmtt) REVERT: B 730 GLU cc_start: 0.7455 (tp30) cc_final: 0.7046 (pt0) REVERT: B 839 ILE cc_start: 0.7626 (mm) cc_final: 0.7372 (mp) REVERT: B 845 ARG cc_start: 0.6976 (tpp80) cc_final: 0.6757 (ttm170) REVERT: B 1045 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6465 (ttp) REVERT: C 659 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.4609 (pmm) REVERT: C 836 VAL cc_start: 0.8112 (p) cc_final: 0.7899 (t) REVERT: C 1133 GLU cc_start: 0.7701 (pt0) cc_final: 0.7489 (pt0) REVERT: D 842 ASN cc_start: 0.7217 (t0) cc_final: 0.6974 (t0) REVERT: D 1020 MET cc_start: 0.8569 (mmm) cc_final: 0.8348 (mmp) outliers start: 51 outliers final: 10 residues processed: 382 average time/residue: 1.2784 time to fit residues: 548.4058 Evaluate side-chains 294 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 279 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain D residue 828 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 584 HIS A 911 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 648 HIS B 721 ASN B 726 HIS C 608 ASN C 721 ASN C 842 ASN ** C 891 HIS ** 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 967 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 2.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 19372 Z= 0.419 Angle : 0.958 16.952 26244 Z= 0.477 Chirality : 0.052 0.239 3088 Planarity : 0.006 0.084 3256 Dihedral : 5.371 29.465 2568 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 2.19 % Allowed : 24.57 % Favored : 73.24 % 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 (0.16), residues: 2332 helix: -0.53 (0.12), residues: 1636 sheet: -1.67 (0.86), residues: 40 loop : -2.63 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 867 HIS 0.015 0.002 HIS B 648 PHE 0.021 0.003 PHE D 752 TYR 0.031 0.003 TYR D 623 ARG 0.016 0.001 ARG B 912 *********************** 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 465 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 419 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 774 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8474 (ttt) REVERT: A 849 GLN cc_start: 0.6922 (tp40) cc_final: 0.6433 (tm-30) REVERT: A 1130 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7086 (mtm110) REVERT: B 686 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7406 (ttmt) REVERT: B 747 SER cc_start: 0.8889 (m) cc_final: 0.8451 (p) REVERT: B 824 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6922 (ttp80) REVERT: B 845 ARG cc_start: 0.7034 (tpp80) cc_final: 0.6732 (ttm170) REVERT: B 1122 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7100 (ttm170) REVERT: B 1130 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7238 (mtm110) REVERT: C 558 THR cc_start: 0.9245 (m) cc_final: 0.9040 (p) REVERT: C 743 MET cc_start: 0.8317 (tmm) cc_final: 0.7981 (ttp) REVERT: C 1149 LYS cc_start: 0.8583 (mttm) cc_final: 0.8370 (mttp) REVERT: D 530 GLN cc_start: 0.7493 (tt0) cc_final: 0.7277 (tp40) REVERT: D 534 ASN cc_start: 0.7930 (m110) cc_final: 0.7247 (m110) REVERT: D 601 MET cc_start: 0.7047 (ppp) cc_final: 0.6698 (ptp) REVERT: D 661 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8554 (tptt) REVERT: D 693 GLN cc_start: 0.7977 (pt0) cc_final: 0.7400 (pt0) outliers start: 46 outliers final: 9 residues processed: 448 average time/residue: 1.1215 time to fit residues: 564.9169 Evaluate side-chains 312 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1068 MET Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1069 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 584 HIS A 753 HIS A 911 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 495 GLN B 534 ASN B 648 HIS B 756 ASN ** C 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 ASN C 842 ASN C 888 ASN C 891 HIS D 482 HIS D 491 ASN D 507 ASN D 523 GLN D 568 HIS D 753 HIS D 967 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 2.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19372 Z= 0.181 Angle : 0.686 11.418 26244 Z= 0.340 Chirality : 0.042 0.191 3088 Planarity : 0.004 0.085 3256 Dihedral : 4.565 24.503 2568 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 1.19 % Allowed : 28.99 % Favored : 69.82 % 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: 0.07 (0.13), residues: 1620 sheet: -1.68 (0.85), residues: 40 loop : -2.34 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 867 HIS 0.040 0.001 HIS B 648 PHE 0.019 0.001 PHE D 752 TYR 0.040 0.001 TYR D 623 ARG 0.008 0.001 ARG A 541 ********************** 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 358 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 333 time to evaluate : 2.509 Fit side-chains revert: symmetry clash REVERT: A 774 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8315 (ttt) REVERT: A 849 GLN cc_start: 0.6923 (tp40) cc_final: 0.6477 (tp40) REVERT: A 1130 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.7012 (mtm110) REVERT: B 648 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.6205 (m90) REVERT: B 747 SER cc_start: 0.8904 (m) cc_final: 0.8469 (p) REVERT: B 824 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: B 845 ARG cc_start: 0.6985 (tpp80) cc_final: 0.6754 (ttm170) REVERT: B 1130 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.7158 (mtm110) REVERT: C 617 TYR cc_start: 0.8040 (m-80) cc_final: 0.7816 (m-80) REVERT: C 641 MET cc_start: 0.8615 (mtp) cc_final: 0.8371 (mtp) REVERT: C 723 MET cc_start: 0.8672 (mtt) cc_final: 0.8399 (mtp) REVERT: C 743 MET cc_start: 0.8367 (tmm) cc_final: 0.8076 (ttp) REVERT: C 842 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7160 (t0) REVERT: C 1131 MET cc_start: 0.8842 (ttp) cc_final: 0.8459 (ttm) REVERT: D 530 GLN cc_start: 0.7432 (tt0) cc_final: 0.7176 (tp40) REVERT: D 534 ASN cc_start: 0.7870 (m110) cc_final: 0.7249 (m110) REVERT: D 601 MET cc_start: 0.6942 (ppp) cc_final: 0.6645 (ptp) REVERT: D 693 GLN cc_start: 0.7895 (pt0) cc_final: 0.7307 (pt0) REVERT: D 1020 MET cc_start: 0.8539 (mmm) cc_final: 0.8312 (mmp) REVERT: D 1130 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7404 (mtm180) outliers start: 25 outliers final: 10 residues processed: 346 average time/residue: 1.2264 time to fit residues: 480.4739 Evaluate side-chains 304 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 1069 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 192 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.0270 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 0.0000 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 495 GLN C 491 ASN C 540 HIS ** C 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114198 restraints weight = 21532.449| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.16 r_work: 0.3026 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 2.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 19372 Z= 0.233 Angle : 0.846 59.157 26244 Z= 0.467 Chirality : 0.045 0.878 3088 Planarity : 0.006 0.177 3256 Dihedral : 4.547 24.115 2568 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.05 % Allowed : 30.37 % Favored : 68.58 % Cbeta Deviations : 0.09 % 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: -0.98 (0.17), residues: 2332 helix: 0.10 (0.13), residues: 1620 sheet: -1.67 (0.85), residues: 40 loop : -2.32 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 867 HIS 0.249 0.003 HIS B 648 PHE 0.019 0.001 PHE D 752 TYR 0.036 0.001 TYR D 623 ARG 0.010 0.000 ARG A1140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7351.24 seconds wall clock time: 130 minutes 43.19 seconds (7843.19 seconds total)