Starting phenix.real_space_refine on Fri Dec 15 06:02:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/12_2023/6bco_7083_updated.pdb" } resolution = 2.88 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= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 19576 2.51 5 N 5308 2.21 5 O 5396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "B ARG 1140": "NH1" <-> "NH2" Residue "B ARG 1146": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C ARG 571": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "C ARG 1140": "NH1" <-> "NH2" Residue "C ARG 1146": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 380": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ARG 571": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 961": "NH1" <-> "NH2" Residue "D ARG 965": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Residue "D ARG 1140": "NH1" <-> "NH2" Residue "D ARG 1146": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30432 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "A" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "C" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "D" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.65, per 1000 atoms: 0.55 Number of scatterers: 30432 At special positions: 0 Unit cell: (153.01, 153.01, 165.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 5396 8.00 N 5308 7.00 C 19576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.05 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.05 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.05 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.05 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: 12.24 Conformation dependent library (CDL) restraints added in 5.9 seconds 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 12 sheets defined 61.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 283 through 295 removed outlier: 4.360A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.713A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.749A pdb=" N SER B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.898A pdb=" N SER B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 452 through 455 No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 585 through 601 Processing helix chain 'B' and resid 606 through 633 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 664 through 667 No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 670 through 681 Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 700 through 703 removed outlier: 3.703A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 766 through 771 Processing helix chain 'B' and resid 775 through 798 Processing helix chain 'B' and resid 808 through 829 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 860 through 879 removed outlier: 3.998A pdb=" N LEU B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 908 removed outlier: 3.531A pdb=" N MET B 896 " --> pdb=" O CYS B 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 903 " --> pdb=" O THR B 899 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL B 908 " --> pdb=" O HIS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 947 removed outlier: 4.316A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS B 924 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 4.615A pdb=" N ARG B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 966 - end of helix removed outlier: 4.012A pdb=" N ILE B 970 " --> pdb=" O PRO B 966 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 971 " --> pdb=" O TYR B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1030 through 1066 removed outlier: 5.313A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1075 No H-bonds generated for 'chain 'B' and resid 1073 through 1075' Processing helix chain 'B' and resid 1077 through 1089 Processing helix chain 'B' and resid 1114 through 1140 Processing helix chain 'B' and resid 1143 through 1161 Processing helix chain 'A' and resid 15 through 19 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 283 through 295 removed outlier: 4.361A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.713A pdb=" N TYR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.749A pdb=" N SER A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.898A pdb=" N SER A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 452 through 455 No H-bonds generated for 'chain 'A' and resid 452 through 455' Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 606 through 633 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 700 through 703 removed outlier: 3.703A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 775 through 798 Processing helix chain 'A' and resid 808 through 829 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 860 through 879 removed outlier: 3.998A pdb=" N LEU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 908 removed outlier: 3.531A pdb=" N MET A 896 " --> pdb=" O CYS A 892 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL A 908 " --> pdb=" O HIS A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 947 removed outlier: 4.316A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 971 removed outlier: 4.615A pdb=" N ARG A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Proline residue: A 966 - end of helix removed outlier: 4.013A pdb=" N ILE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A 971 " --> pdb=" O TYR A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1030 through 1066 removed outlier: 5.313A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1075 No H-bonds generated for 'chain 'A' and resid 1073 through 1075' Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1114 through 1140 Processing helix chain 'A' and resid 1143 through 1161 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 144 through 150 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 283 through 295 removed outlier: 4.360A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.713A pdb=" N TYR C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 407 through 413 removed outlier: 3.749A pdb=" N SER C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.897A pdb=" N SER C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'C' and resid 452 through 455 No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 558 through 568 Processing helix chain 'C' and resid 572 through 581 Processing helix chain 'C' and resid 585 through 601 Processing helix chain 'C' and resid 606 through 633 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 664 through 667 No H-bonds generated for 'chain 'C' and resid 664 through 667' Processing helix chain 'C' and resid 670 through 681 Processing helix chain 'C' and resid 690 through 698 Processing helix chain 'C' and resid 700 through 703 removed outlier: 3.704A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 766 through 771 Processing helix chain 'C' and resid 775 through 798 Processing helix chain 'C' and resid 808 through 829 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 860 through 879 removed outlier: 3.997A pdb=" N LEU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 908 removed outlier: 3.532A pdb=" N MET C 896 " --> pdb=" O CYS C 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 897 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU C 903 " --> pdb=" O THR C 899 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS C 904 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL C 908 " --> pdb=" O HIS C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 947 removed outlier: 4.316A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET C 922 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS C 924 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 971 removed outlier: 4.615A pdb=" N ARG C 965 " --> pdb=" O ARG C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix removed outlier: 4.013A pdb=" N ILE C 970 " --> pdb=" O PRO C 966 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE C 971 " --> pdb=" O TYR C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1030 through 1066 removed outlier: 5.312A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1075 No H-bonds generated for 'chain 'C' and resid 1073 through 1075' Processing helix chain 'C' and resid 1077 through 1089 Processing helix chain 'C' and resid 1114 through 1140 Processing helix chain 'C' and resid 1143 through 1161 Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 133 through 141 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 283 through 295 removed outlier: 4.361A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.713A pdb=" N TYR D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 391 through 403 Processing helix chain 'D' and resid 407 through 413 removed outlier: 3.749A pdb=" N SER D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.898A pdb=" N SER D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'D' and resid 452 through 455 No H-bonds generated for 'chain 'D' and resid 452 through 455' Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 558 through 568 Processing helix chain 'D' and resid 572 through 581 Processing helix chain 'D' and resid 585 through 601 Processing helix chain 'D' and resid 606 through 633 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 664 through 667 No H-bonds generated for 'chain 'D' and resid 664 through 667' Processing helix chain 'D' and resid 670 through 681 Processing helix chain 'D' and resid 690 through 698 Processing helix chain 'D' and resid 700 through 703 removed outlier: 3.704A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 766 through 771 Processing helix chain 'D' and resid 775 through 798 Processing helix chain 'D' and resid 808 through 829 Processing helix chain 'D' and resid 849 through 856 Processing helix chain 'D' and resid 860 through 879 removed outlier: 3.998A pdb=" N LEU D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 908 removed outlier: 3.531A pdb=" N MET D 896 " --> pdb=" O CYS D 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 897 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 903 " --> pdb=" O THR D 899 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS D 904 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR D 907 " --> pdb=" O LEU D 903 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL D 908 " --> pdb=" O HIS D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 947 removed outlier: 4.316A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET D 923 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS D 924 " --> pdb=" O SER D 920 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 971 removed outlier: 4.614A pdb=" N ARG D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Proline residue: D 966 - end of helix removed outlier: 4.012A pdb=" N ILE D 970 " --> pdb=" O PRO D 966 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE D 971 " --> pdb=" O TYR D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1030 through 1066 removed outlier: 5.312A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1075 No H-bonds generated for 'chain 'D' and resid 1073 through 1075' Processing helix chain 'D' and resid 1077 through 1089 Processing helix chain 'D' and resid 1114 through 1140 Processing helix chain 'D' and resid 1143 through 1161 Processing sheet with id= A, first strand: chain 'B' and resid 21 through 24 Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.529A pdb=" N PHE B 233 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 232 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER B 121 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 275 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU B 123 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 277 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU B 278 " --> pdb=" O PRO B 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 300 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP B 996 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 21 through 24 Processing sheet with id= E, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.529A pdb=" N PHE A 233 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 232 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER A 121 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 275 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU A 123 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 277 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 278 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 300 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP A 996 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 21 through 24 Processing sheet with id= H, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.530A pdb=" N PHE C 233 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 232 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER C 121 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 275 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU C 123 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C 277 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU C 278 " --> pdb=" O PRO C 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 300 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.972A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP C 996 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 21 through 24 Processing sheet with id= K, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.530A pdb=" N PHE D 233 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 232 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER D 121 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 275 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU D 123 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU D 277 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU D 278 " --> pdb=" O PRO D 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU D 300 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP D 996 " --> pdb=" O GLY D 987 " (cutoff:3.500A) 1584 hydrogen bonds defined for protein. 4716 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: 16.65 Time building geometry restraints manager: 12.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8968 1.34 - 1.46: 5868 1.46 - 1.58: 16064 1.58 - 1.70: 20 1.70 - 1.82: 208 Bond restraints: 31128 Sorted by residual: bond pdb=" C4 ATP C2000 " pdb=" C5 ATP C2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP D2000 " pdb=" C5 ATP D2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C PHE D 81 " pdb=" N THR D 82 " ideal model delta sigma weight residual 1.331 1.224 0.106 1.41e-02 5.03e+03 5.65e+01 ... (remaining 31123 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.46: 600 105.46 - 113.14: 16984 113.14 - 120.81: 15457 120.81 - 128.49: 8875 128.49 - 136.17: 308 Bond angle restraints: 42224 Sorted by residual: angle pdb=" PB ATP D2000 " pdb=" O3B ATP D2000 " pdb=" PG ATP D2000 " ideal model delta sigma weight residual 139.87 120.29 19.58 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 120.30 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PA ATP C2000 " pdb=" O3A ATP C2000 " pdb=" PB ATP C2000 " ideal model delta sigma weight residual 136.83 127.20 9.63 1.00e+00 1.00e+00 9.27e+01 ... (remaining 42219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17841 17.81 - 35.63: 546 35.63 - 53.44: 92 53.44 - 71.26: 13 71.26 - 89.07: 36 Dihedral angle restraints: 18528 sinusoidal: 7544 harmonic: 10984 Sorted by residual: dihedral pdb=" CA ILE C 279 " pdb=" C ILE C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual -180.00 -153.14 -26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE B 279 " pdb=" C ILE B 279 " pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 279 " pdb=" C ILE A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 18525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3903 0.065 - 0.131: 786 0.131 - 0.196: 51 0.196 - 0.261: 4 0.261 - 0.327: 12 Chirality restraints: 4756 Sorted by residual: chirality pdb=" CB VAL A1003 " pdb=" CA VAL A1003 " pdb=" CG1 VAL A1003 " pdb=" CG2 VAL A1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL B1003 " pdb=" CA VAL B1003 " pdb=" CG1 VAL B1003 " pdb=" CG2 VAL B1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL C1003 " pdb=" CA VAL C1003 " pdb=" CG1 VAL C1003 " pdb=" CG2 VAL C1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 4753 not shown) Planarity restraints: 5300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.026 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP B 816 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 816 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP C 816 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 816 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 816 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 816 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 816 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 816 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 816 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 816 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.003 2.00e-02 2.50e+03 ... (remaining 5297 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8364 2.81 - 3.33: 26886 3.33 - 3.85: 47429 3.85 - 4.38: 55458 4.38 - 4.90: 95712 Nonbonded interactions: 233849 Sorted by model distance: nonbonded pdb=" O ARG A 354 " pdb=" OG1 THR A 357 " model vdw 2.286 2.440 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.286 2.440 nonbonded pdb=" O ARG B 354 " pdb=" OG1 THR B 357 " model vdw 2.286 2.440 nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 21 " pdb=" OE2 GLU A 70 " model vdw 2.294 2.440 ... (remaining 233844 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: 0.820 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: 0.040 Extract box with map and model: 5.520 Check model and map are aligned: 0.490 Set scattering table: 0.240 Process input model: 89.640 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.220 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:23.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.007 0.106 31128 Z= 0.466 Angle : 0.976 19.577 42224 Z= 0.573 Chirality : 0.052 0.327 4756 Planarity : 0.007 0.060 5300 Dihedral : 10.396 89.071 11412 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.37 % Allowed : 2.47 % Favored : 97.16 % 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: -4.72 (0.09), residues: 3744 helix: -3.11 (0.06), residues: 2360 sheet: -1.50 (0.34), residues: 232 loop : -3.05 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 816 HIS 0.009 0.002 HIS A1080 PHE 0.023 0.003 PHE B1039 TYR 0.017 0.002 TYR D 339 ARG 0.017 0.001 ARG B1146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 655 time to evaluate : 3.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 663 average time/residue: 1.6223 time to fit residues: 1241.7386 Evaluate side-chains 306 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 4.9758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 221 optimal weight: 9.9990 chunk 345 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 175 GLN B 197 ASN B 248 ASN B 296 GLN B 349 GLN B 405 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN B 904 HIS B1010 GLN B1013 ASN A 90 ASN A 197 ASN A 248 ASN A 296 GLN A 349 GLN A 405 ASN A 420 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A 904 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 90 ASN C 175 GLN C 197 ASN C 248 ASN C 296 GLN C 405 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN C 802 GLN C 904 HIS C1010 GLN C1013 ASN D 90 ASN D 175 GLN D 197 ASN D 248 ASN D 296 GLN D 349 GLN D 405 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN D 904 HIS D1010 GLN D1013 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31128 Z= 0.202 Angle : 0.599 8.549 42224 Z= 0.304 Chirality : 0.039 0.158 4756 Planarity : 0.005 0.059 5300 Dihedral : 7.656 84.102 4308 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.77 % Allowed : 9.49 % Favored : 87.73 % 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: -1.64 (0.12), residues: 3744 helix: -0.28 (0.10), residues: 2384 sheet: -0.84 (0.31), residues: 252 loop : -2.81 (0.15), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 816 HIS 0.003 0.001 HIS C 795 PHE 0.023 0.002 PHE C 793 TYR 0.019 0.001 TYR A 228 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 360 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 38 residues processed: 421 average time/residue: 1.3738 time to fit residues: 685.2866 Evaluate side-chains 306 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 3.058 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 1 average time/residue: 0.4065 time to fit residues: 4.9064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 234 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 345 optimal weight: 5.9990 chunk 373 optimal weight: 0.0570 chunk 307 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 GLN A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A1010 GLN C 148 GLN C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31128 Z= 0.296 Angle : 0.606 10.510 42224 Z= 0.309 Chirality : 0.041 0.150 4756 Planarity : 0.005 0.056 5300 Dihedral : 7.289 88.381 4308 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.51 % Allowed : 11.10 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3744 helix: 0.83 (0.10), residues: 2388 sheet: -0.48 (0.32), residues: 252 loop : -2.64 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1054 HIS 0.004 0.001 HIS C1127 PHE 0.032 0.002 PHE A 793 TYR 0.023 0.002 TYR B 104 ARG 0.008 0.001 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 282 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 51 residues processed: 364 average time/residue: 1.3535 time to fit residues: 587.9612 Evaluate side-chains 298 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 3.510 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 38 residues processed: 13 average time/residue: 0.3655 time to fit residues: 12.7091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 164 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 346 optimal weight: 0.8980 chunk 367 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 328 optimal weight: 0.0020 chunk 98 optimal weight: 20.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 584 ASN B1013 ASN B1028 ASN A 148 GLN A 175 GLN A 584 ASN A1013 ASN A1028 ASN C 175 GLN C 584 ASN C1013 ASN C1028 ASN D 175 GLN D 584 ASN D1013 ASN D1028 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 31128 Z= 0.142 Angle : 0.495 13.369 42224 Z= 0.254 Chirality : 0.035 0.139 4756 Planarity : 0.004 0.047 5300 Dihedral : 6.861 87.423 4308 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.87 % Allowed : 12.18 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3744 helix: 1.69 (0.11), residues: 2400 sheet: -0.49 (0.32), residues: 252 loop : -2.51 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1054 HIS 0.002 0.001 HIS B1127 PHE 0.018 0.001 PHE C 250 TYR 0.014 0.001 TYR C 104 ARG 0.006 0.000 ARG D 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 319 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 38 residues processed: 394 average time/residue: 1.4061 time to fit residues: 658.9331 Evaluate side-chains 290 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 252 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 37 residues processed: 1 average time/residue: 0.3422 time to fit residues: 5.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN C 175 GLN C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN D 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 31128 Z= 0.523 Angle : 0.728 14.187 42224 Z= 0.370 Chirality : 0.048 0.238 4756 Planarity : 0.006 0.065 5300 Dihedral : 7.296 88.887 4308 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.18 % Allowed : 13.53 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3744 helix: 1.22 (0.11), residues: 2392 sheet: -0.65 (0.31), residues: 260 loop : -2.61 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1054 HIS 0.006 0.002 HIS C1127 PHE 0.036 0.003 PHE A 793 TYR 0.020 0.003 TYR B 228 ARG 0.008 0.001 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 249 time to evaluate : 3.285 Fit side-chains outliers start: 103 outliers final: 68 residues processed: 326 average time/residue: 1.3061 time to fit residues: 511.2433 Evaluate side-chains 299 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 231 time to evaluate : 3.726 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 54 residues processed: 18 average time/residue: 0.4484 time to fit residues: 16.9721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 367 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 175 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 148 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C1013 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31128 Z= 0.193 Angle : 0.537 11.611 42224 Z= 0.275 Chirality : 0.038 0.144 4756 Planarity : 0.004 0.053 5300 Dihedral : 6.937 88.361 4308 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.96 % Allowed : 13.59 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3744 helix: 1.69 (0.11), residues: 2400 sheet: -0.49 (0.32), residues: 252 loop : -2.52 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1054 HIS 0.004 0.001 HIS B1127 PHE 0.015 0.001 PHE A 793 TYR 0.014 0.001 TYR B 228 ARG 0.006 0.000 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 279 time to evaluate : 3.816 Fit side-chains outliers start: 96 outliers final: 57 residues processed: 346 average time/residue: 1.3508 time to fit residues: 562.1035 Evaluate side-chains 298 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 3.330 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 46 residues processed: 11 average time/residue: 0.6697 time to fit residues: 14.8628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 209 optimal weight: 0.0020 chunk 268 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN A 148 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 669 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31128 Z= 0.261 Angle : 0.570 11.131 42224 Z= 0.293 Chirality : 0.040 0.140 4756 Planarity : 0.005 0.053 5300 Dihedral : 6.907 89.558 4308 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.93 % Allowed : 14.03 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3744 helix: 1.75 (0.11), residues: 2408 sheet: -0.73 (0.31), residues: 260 loop : -2.50 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1054 HIS 0.004 0.001 HIS C1127 PHE 0.020 0.002 PHE A 793 TYR 0.014 0.002 TYR A 228 ARG 0.008 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 257 time to evaluate : 3.744 Fit side-chains outliers start: 95 outliers final: 68 residues processed: 320 average time/residue: 1.2440 time to fit residues: 486.9580 Evaluate side-chains 304 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 50 residues processed: 18 average time/residue: 0.6521 time to fit residues: 20.6236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 706 ASN A 148 GLN A 175 GLN A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 706 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 706 ASN D 148 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 706 ASN D1013 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 31128 Z= 0.154 Angle : 0.504 9.783 42224 Z= 0.259 Chirality : 0.036 0.133 4756 Planarity : 0.004 0.046 5300 Dihedral : 6.716 87.667 4308 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 14.86 % Favored : 82.55 % 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: 1.10 (0.14), residues: 3744 helix: 2.11 (0.11), residues: 2412 sheet: -0.47 (0.32), residues: 252 loop : -2.33 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 134 HIS 0.004 0.001 HIS A1127 PHE 0.010 0.001 PHE C 627 TYR 0.015 0.001 TYR C 339 ARG 0.005 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 287 time to evaluate : 2.981 Fit side-chains outliers start: 84 outliers final: 39 residues processed: 357 average time/residue: 1.1629 time to fit residues: 501.4116 Evaluate side-chains 287 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 37 residues processed: 2 average time/residue: 0.2331 time to fit residues: 4.4084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 10.0000 chunk 350 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 chunk 341 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 669 GLN B 706 ASN B1013 ASN A 420 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 669 GLN A 706 ASN A1013 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN D 148 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 706 ASN D1013 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31128 Z= 0.249 Angle : 0.567 10.631 42224 Z= 0.291 Chirality : 0.039 0.134 4756 Planarity : 0.005 0.054 5300 Dihedral : 6.771 88.658 4308 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.03 % Allowed : 16.09 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3744 helix: 1.98 (0.11), residues: 2408 sheet: -0.60 (0.32), residues: 260 loop : -2.43 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 134 HIS 0.004 0.001 HIS C1127 PHE 0.027 0.002 PHE B 250 TYR 0.015 0.002 TYR D 339 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 256 time to evaluate : 2.603 Fit side-chains outliers start: 66 outliers final: 47 residues processed: 313 average time/residue: 1.1165 time to fit residues: 422.0886 Evaluate side-chains 283 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 5 average time/residue: 0.6268 time to fit residues: 7.1521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 378 optimal weight: 1.9990 chunk 348 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: