Starting phenix.real_space_refine on Sun Apr 14 05:02:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/04_2024/6bco_7083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/04_2024/6bco_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_7083/04_2024/6bco_7083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/04_2024/6bco_7083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/04_2024/6bco_7083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bco_7083/04_2024/6bco_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 18.16, per 1000 atoms: 0.60 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: 13.26 Conformation dependent library (CDL) restraints added in 5.3 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: 7.08 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: 10.70 Time building geometry restraints manager: 14.34 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.700 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 84.130 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.180 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.290 ------------------------------------------------------------------------------- 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 : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7443 (mt0) cc_final: 0.6845 (tp40) REVERT: B 214 TRP cc_start: 0.7026 (p-90) cc_final: 0.6819 (p-90) REVERT: B 864 ASP cc_start: 0.6749 (t0) cc_final: 0.6530 (t0) REVERT: B 952 ASP cc_start: 0.7296 (m-30) cc_final: 0.7087 (m-30) REVERT: A 79 LEU cc_start: 0.7271 (tm) cc_final: 0.6711 (mm) REVERT: A 175 GLN cc_start: 0.7351 (mt0) cc_final: 0.6908 (tp40) REVERT: A 214 TRP cc_start: 0.6919 (p-90) cc_final: 0.6698 (p-90) REVERT: A 864 ASP cc_start: 0.6685 (t0) cc_final: 0.6476 (t0) REVERT: A 952 ASP cc_start: 0.7323 (m-30) cc_final: 0.7116 (m-30) REVERT: C 156 THR cc_start: 0.8216 (m) cc_final: 0.7988 (p) REVERT: C 175 GLN cc_start: 0.7450 (mt0) cc_final: 0.6834 (tp40) REVERT: C 864 ASP cc_start: 0.6694 (t0) cc_final: 0.6478 (t0) REVERT: C 952 ASP cc_start: 0.7221 (m-30) cc_final: 0.6992 (m-30) REVERT: D 175 GLN cc_start: 0.7440 (mt0) cc_final: 0.6845 (tp40) REVERT: D 214 TRP cc_start: 0.7023 (p-90) cc_final: 0.6822 (p-90) REVERT: D 864 ASP cc_start: 0.6748 (t0) cc_final: 0.6514 (t0) REVERT: D 952 ASP cc_start: 0.7291 (m-30) cc_final: 0.7083 (m-30) outliers start: 12 outliers final: 4 residues processed: 663 average time/residue: 1.6504 time to fit residues: 1260.9235 Evaluate side-chains 318 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 314 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 1008 VAL 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: 10.0000 chunk 159 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 297 optimal weight: 0.1980 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: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN 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 A1013 ASN C 90 ASN 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 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31128 Z= 0.199 Angle : 0.598 8.376 42224 Z= 0.304 Chirality : 0.039 0.159 4756 Planarity : 0.005 0.059 5300 Dihedral : 7.754 83.632 4312 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 9.28 % Favored : 87.98 % 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: -1.63 (0.12), residues: 3744 helix: -0.27 (0.10), residues: 2368 sheet: -0.87 (0.31), residues: 252 loop : -2.78 (0.15), residues: 1124 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 0.022 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 458 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 369 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.5937 (mmt180) cc_final: 0.5697 (mpt180) REVERT: B 864 ASP cc_start: 0.6607 (t0) cc_final: 0.6150 (m-30) REVERT: A 86 ARG cc_start: 0.5943 (mmt180) cc_final: 0.5706 (mpt180) REVERT: A 194 VAL cc_start: 0.7076 (t) cc_final: 0.6851 (m) REVERT: A 359 LYS cc_start: 0.6845 (tptm) cc_final: 0.6069 (tppt) REVERT: A 416 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6062 (mtp180) REVERT: A 864 ASP cc_start: 0.6659 (t0) cc_final: 0.6294 (t0) REVERT: C 86 ARG cc_start: 0.5940 (mmt180) cc_final: 0.5675 (mpt180) REVERT: C 175 GLN cc_start: 0.7458 (mt0) cc_final: 0.7045 (tp40) REVERT: C 864 ASP cc_start: 0.6644 (t0) cc_final: 0.6273 (t0) REVERT: D 86 ARG cc_start: 0.5946 (mmt180) cc_final: 0.5711 (mpt180) REVERT: D 194 VAL cc_start: 0.7187 (t) cc_final: 0.6926 (m) REVERT: D 864 ASP cc_start: 0.6608 (t0) cc_final: 0.6155 (m-30) outliers start: 89 outliers final: 38 residues processed: 429 average time/residue: 1.4118 time to fit residues: 715.3756 Evaluate side-chains 320 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 281 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 1006 SER Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 1006 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 1006 SER Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 584 ASN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 1006 SER Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 234 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 345 optimal weight: 4.9990 chunk 373 optimal weight: 0.0170 chunk 307 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- 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 584 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 GLN A 148 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31128 Z= 0.270 Angle : 0.590 10.047 42224 Z= 0.301 Chirality : 0.040 0.151 4756 Planarity : 0.005 0.055 5300 Dihedral : 7.414 88.731 4312 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.24 % Allowed : 11.19 % Favored : 85.57 % 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: -0.34 (0.13), residues: 3744 helix: 0.87 (0.10), residues: 2392 sheet: -0.51 (0.32), residues: 252 loop : -2.63 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1054 HIS 0.004 0.001 HIS B1127 PHE 0.032 0.002 PHE A 793 TYR 0.022 0.002 TYR B 104 ARG 0.007 0.000 ARG B 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 401 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 296 time to evaluate : 3.454 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: B 635 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 864 ASP cc_start: 0.6801 (t0) cc_final: 0.6229 (m-30) REVERT: A 416 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6142 (mtp180) REVERT: A 635 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 864 ASP cc_start: 0.6683 (t0) cc_final: 0.6274 (m-30) REVERT: C 86 ARG cc_start: 0.5870 (mmt180) cc_final: 0.5620 (mpt180) REVERT: C 289 ILE cc_start: 0.8405 (mt) cc_final: 0.8171 (mt) REVERT: C 359 LYS cc_start: 0.6083 (tppt) cc_final: 0.5593 (tptt) REVERT: C 635 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: C 864 ASP cc_start: 0.6670 (t0) cc_final: 0.6221 (m-30) REVERT: D 86 ARG cc_start: 0.5928 (mmt180) cc_final: 0.5681 (mpt180) REVERT: D 635 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: D 864 ASP cc_start: 0.6801 (t0) cc_final: 0.6238 (m-30) outliers start: 105 outliers final: 39 residues processed: 368 average time/residue: 1.4566 time to fit residues: 632.5291 Evaluate side-chains 298 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1087 TRP Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1141 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 346 optimal weight: 0.7980 chunk 367 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN B1028 ASN A 175 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1028 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN C1028 ASN D 175 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN D1028 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31128 Z= 0.200 Angle : 0.536 13.581 42224 Z= 0.273 Chirality : 0.038 0.138 4756 Planarity : 0.004 0.053 5300 Dihedral : 7.209 89.383 4312 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.77 % Allowed : 12.58 % Favored : 84.65 % 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: 0.35 (0.14), residues: 3744 helix: 1.49 (0.11), residues: 2396 sheet: -0.49 (0.32), residues: 252 loop : -2.53 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1054 HIS 0.003 0.001 HIS B1127 PHE 0.018 0.001 PHE A 793 TYR 0.014 0.001 TYR D 228 ARG 0.006 0.000 ARG A 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 384 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 294 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 826 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7386 (ttt-90) REVERT: B 864 ASP cc_start: 0.6791 (t0) cc_final: 0.6129 (m-30) REVERT: A 359 LYS cc_start: 0.7143 (tptt) cc_final: 0.6422 (tppt) REVERT: A 416 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6134 (mtp180) REVERT: A 864 ASP cc_start: 0.6790 (t0) cc_final: 0.6173 (m-30) REVERT: C 864 ASP cc_start: 0.6806 (t0) cc_final: 0.6132 (m-30) REVERT: D 826 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.7384 (ttt-90) REVERT: D 864 ASP cc_start: 0.6787 (t0) cc_final: 0.6139 (m-30) outliers start: 90 outliers final: 31 residues processed: 355 average time/residue: 1.4828 time to fit residues: 619.9265 Evaluate side-chains 295 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 263 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1087 TRP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 313 optimal weight: 30.0000 chunk 253 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN B 420 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN C 175 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN D 261 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 31128 Z= 0.491 Angle : 0.705 14.192 42224 Z= 0.359 Chirality : 0.046 0.171 4756 Planarity : 0.006 0.067 5300 Dihedral : 7.516 88.953 4312 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.08 % Allowed : 13.41 % Favored : 83.51 % 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: -0.04 (0.14), residues: 3744 helix: 1.18 (0.11), residues: 2392 sheet: -0.73 (0.31), residues: 260 loop : -2.64 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1054 HIS 0.006 0.002 HIS A1127 PHE 0.033 0.003 PHE C 793 TYR 0.025 0.003 TYR D 228 ARG 0.008 0.001 ARG C1058 *********************** 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 362 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 3.698 Fit side-chains REVERT: B 300 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 344 ASP cc_start: 0.5514 (m-30) cc_final: 0.5063 (t0) REVERT: B 635 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 300 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 344 ASP cc_start: 0.5510 (m-30) cc_final: 0.5157 (t0) REVERT: A 416 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6211 (mtp180) REVERT: A 635 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 183 LYS cc_start: 0.7073 (mmpt) cc_final: 0.6772 (mmtt) REVERT: C 344 ASP cc_start: 0.5575 (m-30) cc_final: 0.5116 (t0) REVERT: C 635 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: D 300 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7686 (tt) REVERT: D 344 ASP cc_start: 0.5517 (m-30) cc_final: 0.5075 (t0) REVERT: D 635 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7276 (mp0) outliers start: 100 outliers final: 53 residues processed: 330 average time/residue: 1.3837 time to fit residues: 543.4368 Evaluate side-chains 295 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 234 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1087 TRP Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1141 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1141 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 5.9990 chunk 330 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 367 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 148 GLN A 175 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 175 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 175 GLN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7956 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31128 Z= 0.212 Angle : 0.546 11.638 42224 Z= 0.279 Chirality : 0.038 0.143 4756 Planarity : 0.005 0.054 5300 Dihedral : 7.188 88.715 4312 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.53 % Allowed : 14.27 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3744 helix: 1.59 (0.11), residues: 2424 sheet: -0.62 (0.32), residues: 252 loop : -2.52 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1054 HIS 0.004 0.001 HIS B1127 PHE 0.015 0.001 PHE C 250 TYR 0.015 0.001 TYR B 228 ARG 0.006 0.000 ARG B 198 *********************** 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 355 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 273 time to evaluate : 3.735 Fit side-chains REVERT: B 141 ARG cc_start: 0.6900 (ppt90) cc_final: 0.6601 (ptm-80) REVERT: B 300 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7699 (tt) REVERT: B 344 ASP cc_start: 0.5447 (m-30) cc_final: 0.5045 (t0) REVERT: B 518 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5299 (mtm-85) REVERT: A 141 ARG cc_start: 0.6998 (ppt90) cc_final: 0.6683 (ptm-80) REVERT: A 183 LYS cc_start: 0.7224 (mmpt) cc_final: 0.6876 (mmtt) REVERT: A 300 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 344 ASP cc_start: 0.5408 (m-30) cc_final: 0.5083 (t0) REVERT: A 359 LYS cc_start: 0.7017 (tptt) cc_final: 0.6365 (tppt) REVERT: A 416 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6167 (mtp180) REVERT: C 300 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7619 (tt) REVERT: C 344 ASP cc_start: 0.5445 (m-30) cc_final: 0.5051 (t0) REVERT: D 91 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6869 (t80) REVERT: D 141 ARG cc_start: 0.6907 (ppt90) cc_final: 0.6602 (ptm-80) REVERT: D 300 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7698 (tt) REVERT: D 344 ASP cc_start: 0.5449 (m-30) cc_final: 0.5056 (t0) outliers start: 82 outliers final: 47 residues processed: 324 average time/residue: 1.4891 time to fit residues: 569.9105 Evaluate side-chains 301 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 205 optimal weight: 0.0370 chunk 366 optimal weight: 0.6980 chunk 229 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- 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 669 GLN B 706 ASN B1013 ASN A 148 GLN A 175 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN C 706 ASN C1013 ASN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3603 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= 0.172 Angle : 0.511 10.680 42224 Z= 0.261 Chirality : 0.037 0.138 4756 Planarity : 0.004 0.048 5300 Dihedral : 6.993 88.038 4312 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.10 % Allowed : 14.55 % Favored : 83.35 % 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: 1.97 (0.11), residues: 2408 sheet: -0.57 (0.32), residues: 252 loop : -2.43 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1054 HIS 0.003 0.001 HIS D1127 PHE 0.014 0.001 PHE C 250 TYR 0.013 0.001 TYR D 339 ARG 0.005 0.000 ARG C 141 *********************** 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 362 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 3.586 Fit side-chains REVERT: B 141 ARG cc_start: 0.6894 (ppt90) cc_final: 0.6640 (ptm-80) REVERT: B 183 LYS cc_start: 0.7460 (mptt) cc_final: 0.7032 (tptt) REVERT: B 300 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7680 (tt) REVERT: B 359 LYS cc_start: 0.5650 (tppt) cc_final: 0.5163 (tptt) REVERT: B 518 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5407 (mtm-85) REVERT: A 91 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6697 (t80) REVERT: A 141 ARG cc_start: 0.6974 (ppt90) cc_final: 0.6733 (ptm-80) REVERT: A 175 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6997 (mm-40) REVERT: A 300 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7671 (tt) REVERT: C 300 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7701 (tt) REVERT: C 344 ASP cc_start: 0.5654 (m-30) cc_final: 0.5178 (t0) REVERT: C 518 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5431 (mtm-85) REVERT: C 1090 ARG cc_start: 0.6158 (ttp-170) cc_final: 0.5947 (ttp-170) REVERT: D 91 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6686 (t80) REVERT: D 141 ARG cc_start: 0.6892 (ppt90) cc_final: 0.6644 (ptm-80) REVERT: D 183 LYS cc_start: 0.7461 (mptt) cc_final: 0.7030 (tptt) REVERT: D 300 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7627 (tt) REVERT: D 359 LYS cc_start: 0.5653 (tppt) cc_final: 0.5171 (tptt) outliers start: 68 outliers final: 41 residues processed: 340 average time/residue: 1.4513 time to fit residues: 585.2255 Evaluate side-chains 303 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 706 ASN B1013 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 HIS A 669 GLN A 706 ASN A1013 ASN ** C 425 HIS ** 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 706 ASN D1013 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3605 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= 0.279 Angle : 0.582 10.629 42224 Z= 0.298 Chirality : 0.040 0.140 4756 Planarity : 0.005 0.067 5300 Dihedral : 7.064 89.244 4312 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.56 % Allowed : 14.98 % Favored : 82.46 % 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: 0.74 (0.14), residues: 3744 helix: 1.86 (0.11), residues: 2404 sheet: -0.69 (0.32), residues: 260 loop : -2.50 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 134 HIS 0.006 0.001 HIS A 174 PHE 0.029 0.002 PHE B 250 TYR 0.016 0.002 TYR A 228 ARG 0.008 0.000 ARG B 337 *********************** 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 347 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 264 time to evaluate : 3.801 Fit side-chains REVERT: B 141 ARG cc_start: 0.6933 (ppt90) cc_final: 0.6571 (ptm-80) REVERT: B 300 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7679 (tt) REVERT: B 518 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5376 (mtm-85) REVERT: A 91 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 141 ARG cc_start: 0.7016 (ppt90) cc_final: 0.6664 (ptm-80) REVERT: A 300 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7662 (tt) REVERT: A 344 ASP cc_start: 0.5545 (m-30) cc_final: 0.5176 (t0) REVERT: C 194 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7217 (p) REVERT: C 300 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7708 (tt) REVERT: C 344 ASP cc_start: 0.5680 (m-30) cc_final: 0.5199 (t0) REVERT: C 518 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5415 (mtm-85) REVERT: D 91 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6708 (t80) REVERT: D 141 ARG cc_start: 0.6937 (ppt90) cc_final: 0.6573 (ptm-80) REVERT: D 300 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7692 (tt) outliers start: 83 outliers final: 53 residues processed: 324 average time/residue: 1.4544 time to fit residues: 557.5278 Evaluate side-chains 304 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP 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: 10.0000 chunk 341 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 706 ASN B1013 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 31128 Z= 0.361 Angle : 0.636 10.902 42224 Z= 0.325 Chirality : 0.042 0.146 4756 Planarity : 0.005 0.068 5300 Dihedral : 7.198 88.423 4312 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.25 % Allowed : 15.35 % Favored : 82.40 % 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: 0.45 (0.14), residues: 3744 helix: 1.57 (0.11), residues: 2424 sheet: -0.76 (0.31), residues: 260 loop : -2.53 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1054 HIS 0.005 0.002 HIS A1127 PHE 0.025 0.002 PHE B 250 TYR 0.019 0.002 TYR A 228 ARG 0.006 0.001 ARG C 597 *********************** 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 330 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 257 time to evaluate : 3.358 Fit side-chains REVERT: B 141 ARG cc_start: 0.6950 (ppt90) cc_final: 0.6550 (ptm-80) REVERT: B 300 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 344 ASP cc_start: 0.5972 (m-30) cc_final: 0.5458 (t0) REVERT: B 518 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5396 (mtm-85) REVERT: A 91 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6824 (t80) REVERT: A 141 ARG cc_start: 0.7028 (ppt90) cc_final: 0.6643 (ptm-80) REVERT: A 300 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7674 (tt) REVERT: A 344 ASP cc_start: 0.5802 (m-30) cc_final: 0.5438 (t0) REVERT: A 635 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 194 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7146 (p) REVERT: C 300 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7702 (tt) REVERT: C 344 ASP cc_start: 0.5828 (m-30) cc_final: 0.5392 (t0) REVERT: C 359 LYS cc_start: 0.5910 (tptt) cc_final: 0.5383 (tptt) REVERT: C 518 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5377 (mtm-85) REVERT: D 91 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6797 (t80) REVERT: D 141 ARG cc_start: 0.6990 (ppt90) cc_final: 0.6596 (ptm-80) REVERT: D 300 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7713 (tt) outliers start: 73 outliers final: 50 residues processed: 308 average time/residue: 1.3734 time to fit residues: 500.7134 Evaluate side-chains 297 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 237 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 8.9990 chunk 360 optimal weight: 0.1980 chunk 220 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 301 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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 706 ASN B1013 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31128 Z= 0.335 Angle : 0.617 10.566 42224 Z= 0.316 Chirality : 0.041 0.139 4756 Planarity : 0.005 0.062 5300 Dihedral : 7.150 88.131 4312 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.10 % Allowed : 15.69 % Favored : 82.21 % 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: 0.43 (0.14), residues: 3744 helix: 1.55 (0.11), residues: 2420 sheet: -0.73 (0.32), residues: 260 loop : -2.50 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1054 HIS 0.005 0.001 HIS C1127 PHE 0.026 0.002 PHE B 250 TYR 0.018 0.002 TYR B 228 ARG 0.005 0.001 ARG B 597 ********************** REFINEMENT MACRO_CYCLE 10 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 312 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 244 time to evaluate : 3.361 Fit side-chains REVERT: B 141 ARG cc_start: 0.6900 (ppt90) cc_final: 0.6501 (ptm-80) REVERT: B 300 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 344 ASP cc_start: 0.5725 (m-30) cc_final: 0.5309 (t0) REVERT: B 518 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5439 (mtm-85) REVERT: A 91 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 141 ARG cc_start: 0.6972 (ppt90) cc_final: 0.6620 (ptm-80) REVERT: A 300 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7735 (tt) REVERT: A 344 ASP cc_start: 0.5754 (m-30) cc_final: 0.5420 (t0) REVERT: A 635 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: C 194 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7199 (p) REVERT: C 300 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7711 (tt) REVERT: C 344 ASP cc_start: 0.5850 (m-30) cc_final: 0.5426 (t0) REVERT: C 359 LYS cc_start: 0.5741 (tptt) cc_final: 0.5456 (tptt) REVERT: C 518 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5419 (mtm-85) REVERT: D 91 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6828 (t80) REVERT: D 141 ARG cc_start: 0.6930 (ppt90) cc_final: 0.6556 (ptm-80) REVERT: D 300 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7737 (tt) REVERT: D 344 ASP cc_start: 0.5733 (m-30) cc_final: 0.5323 (t0) outliers start: 68 outliers final: 51 residues processed: 289 average time/residue: 1.5278 time to fit residues: 523.4192 Evaluate side-chains 291 residues out of total 3244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1159 LYS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C 827 GLN C1013 ASN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113215 restraints weight = 40273.961| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3039 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3820 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: