Starting phenix.real_space_refine on Sun Dec 10 05:12:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/12_2023/6zy6_11551_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.065 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 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1148": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.06, per 1000 atoms: 0.45 Number of scatterers: 13504 At special positions: 0 Unit cell: (100.969, 119.053, 122.067, 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 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 12 sheets defined 43.4% alpha, 5.8% beta 30 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 80.63 Creating SS restraints... Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.970A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.683A pdb=" N ILE A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 545 through 558 removed outlier: 3.643A pdb=" N ILE A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 566 removed outlier: 3.691A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.585A pdb=" N GLU A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 643 through 653 removed outlier: 4.175A pdb=" N ALA A 652 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 678 Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 744 through 754 removed outlier: 3.582A pdb=" N GLY A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 772 Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.891A pdb=" N HIS A 824 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 removed outlier: 4.074A pdb=" N ASN A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.708A pdb=" N ASN A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.684A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix Processing helix chain 'A' and resid 974 through 983 removed outlier: 3.678A pdb=" N ALA A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.950A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1060 removed outlier: 3.606A pdb=" N GLU A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.743A pdb=" N GLN A1094 " --> pdb=" O TRP A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1133 through 1136 Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 3.708A pdb=" N ARG A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A1149 " --> pdb=" O CYS A1145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1191 removed outlier: 4.052A pdb=" N THR A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.969A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 505 through 514 removed outlier: 3.684A pdb=" N ILE B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 545 through 558 removed outlier: 3.641A pdb=" N ILE B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 566 removed outlier: 3.691A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 566' Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.589A pdb=" N GLU B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.173A pdb=" N ALA B 652 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 678 Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 714 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 744 through 754 removed outlier: 3.582A pdb=" N GLY B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 750 " --> pdb=" O GLN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 772 Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 820 through 824 removed outlier: 3.890A pdb=" N HIS B 824 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 removed outlier: 4.076A pdb=" N ASN B 851 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 881 removed outlier: 3.708A pdb=" N ASN B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 4.685A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 974 through 983 removed outlier: 3.680A pdb=" N ALA B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 979 " --> pdb=" O GLU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 1015 through 1037 removed outlier: 3.949A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1060 removed outlier: 3.605A pdb=" N GLU B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1079 Processing helix chain 'B' and resid 1086 through 1094 removed outlier: 3.744A pdb=" N GLN B1094 " --> pdb=" O TRP B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1138 through 1160 removed outlier: 3.708A pdb=" N ARG B1146 " --> pdb=" O ASP B1142 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B1149 " --> pdb=" O CYS B1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B1151 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B1152 " --> pdb=" O ARG B1148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1191 removed outlier: 4.053A pdb=" N THR B1173 " --> pdb=" O GLU B1169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B1174 " --> pdb=" O ASP B1170 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.458A pdb=" N LYS A 535 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU A 459 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET A 537 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 538 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL A 580 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 589 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 578 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 853 through 856 removed outlier: 3.698A pdb=" N ALA A 853 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 906 through 909 Processing sheet with id= E, first strand: chain 'A' and resid 1001 through 1003 removed outlier: 3.970A pdb=" N LEU A1002 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A1010 " --> pdb=" O LEU A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 912 through 914 removed outlier: 5.955A pdb=" N ALA A 914 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE A 923 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 482 through 485 removed outlier: 6.458A pdb=" N LYS B 535 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU B 459 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 537 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 538 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 586 through 589 removed outlier: 3.713A pdb=" N VAL B 580 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 589 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 578 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 853 through 856 removed outlier: 3.696A pdb=" N ALA B 853 " --> pdb=" O ILE B 864 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 906 through 909 Processing sheet with id= K, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 3.967A pdb=" N LEU B1002 " --> pdb=" O LYS B1010 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B1010 " --> pdb=" O LEU B1002 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 912 through 914 removed outlier: 5.956A pdb=" N ALA B 914 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE B 923 " --> pdb=" O ALA B 914 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2441 1.32 - 1.45: 3612 1.45 - 1.57: 7651 1.57 - 1.69: 112 1.69 - 1.81: 92 Bond restraints: 13908 Sorted by residual: bond pdb=" N VAL A 939 " pdb=" CA VAL A 939 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.29e+01 bond pdb=" N VAL B 939 " pdb=" CA VAL B 939 " ideal model delta sigma weight residual 1.458 1.489 -0.032 9.00e-03 1.23e+04 1.24e+01 bond pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.00e-03 1.23e+04 1.15e+01 bond pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta sigma weight residual 1.457 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 bond pdb=" N ILE B 864 " pdb=" CA ILE B 864 " ideal model delta sigma weight residual 1.456 1.485 -0.028 8.70e-03 1.32e+04 1.06e+01 ... (remaining 13903 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.55: 730 106.55 - 113.53: 7716 113.53 - 120.51: 6636 120.51 - 127.49: 3780 127.49 - 134.48: 168 Bond angle restraints: 19030 Sorted by residual: angle pdb=" N ILE B1065 " pdb=" CA ILE B1065 " pdb=" C ILE B1065 " ideal model delta sigma weight residual 111.91 108.89 3.02 8.90e-01 1.26e+00 1.15e+01 angle pdb=" N ILE A1065 " pdb=" CA ILE A1065 " pdb=" C ILE A1065 " ideal model delta sigma weight residual 111.91 108.91 3.00 8.90e-01 1.26e+00 1.14e+01 angle pdb=" C GLY A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 123.33 120.41 2.92 8.70e-01 1.32e+00 1.13e+01 angle pdb=" C GLY B 437 " pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta sigma weight residual 123.33 120.41 2.92 8.70e-01 1.32e+00 1.13e+01 angle pdb=" CA GLU B1066 " pdb=" C GLU B1066 " pdb=" O GLU B1066 " ideal model delta sigma weight residual 122.64 118.66 3.98 1.25e+00 6.40e-01 1.02e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 8145 35.97 - 71.95: 231 71.95 - 107.92: 2 107.92 - 143.89: 4 143.89 - 179.87: 2 Dihedral angle restraints: 8384 sinusoidal: 3964 harmonic: 4420 Sorted by residual: dihedral pdb=" C ASN B 604 " pdb=" N ASN B 604 " pdb=" CA ASN B 604 " pdb=" CB ASN B 604 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" C ASN A 604 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " pdb=" CB ASN A 604 " ideal model delta harmonic sigma weight residual -122.60 -133.41 10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C4' DG D 9 " pdb=" C3' DG D 9 " pdb=" O3' DG D 9 " pdb=" P DT D 10 " ideal model delta sinusoidal sigma weight residual 220.00 40.13 179.87 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1440 0.075 - 0.149: 523 0.149 - 0.224: 121 0.224 - 0.299: 6 0.299 - 0.374: 4 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ASN B 604 " pdb=" N ASN B 604 " pdb=" C ASN B 604 " pdb=" CB ASN B 604 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ASN A 604 " pdb=" N ASN A 604 " pdb=" C ASN A 604 " pdb=" CB ASN A 604 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C9 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" C6 EVP F 101 " pdb=" C8 EVP F 101 " both_signs ideal model delta sigma weight residual False 2.49 2.81 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2091 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 603 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C PRO B 603 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 603 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 604 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 603 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PRO A 603 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 603 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 604 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 617 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C GLY A 617 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 617 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 618 " 0.017 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3925 2.82 - 3.34: 12189 3.34 - 3.86: 21454 3.86 - 4.38: 24409 4.38 - 4.90: 39737 Nonbonded interactions: 101714 Sorted by model distance: nonbonded pdb=" OG SER A1045 " pdb=" OE2 GLU A1152 " model vdw 2.304 2.440 nonbonded pdb=" OG SER B1045 " pdb=" OE2 GLU B1152 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR A 456 " pdb=" O LYS A 480 " model vdw 2.326 2.440 nonbonded pdb=" OG1 THR B 456 " pdb=" O LYS B 480 " model vdw 2.327 2.440 nonbonded pdb=" O ASP A 524 " pdb=" OG SER A 527 " model vdw 2.349 2.440 ... (remaining 101709 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.730 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.270 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.010 0.040 13908 Z= 0.657 Angle : 1.070 5.421 19030 Z= 0.811 Chirality : 0.079 0.374 2094 Planarity : 0.007 0.032 2220 Dihedral : 13.750 179.868 5536 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1512 helix: 1.33 (0.19), residues: 650 sheet: -1.64 (0.44), residues: 154 loop : -1.98 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 664 HIS 0.006 0.001 HIS A 634 PHE 0.008 0.002 PHE A1003 TYR 0.010 0.002 TYR B 590 ARG 0.007 0.001 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.3042 time to fit residues: 176.5515 Evaluate side-chains 189 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 824 HIS A 875 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS B 824 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13908 Z= 0.159 Angle : 0.527 8.277 19030 Z= 0.265 Chirality : 0.038 0.195 2094 Planarity : 0.004 0.033 2220 Dihedral : 17.445 179.886 2420 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -0.40 (0.22), residues: 1512 helix: 1.53 (0.20), residues: 646 sheet: -1.29 (0.45), residues: 154 loop : -1.80 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1090 HIS 0.004 0.001 HIS A 634 PHE 0.010 0.001 PHE A 653 TYR 0.016 0.001 TYR B 686 ARG 0.005 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2561 time to fit residues: 92.4461 Evaluate side-chains 151 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.0770 chunk 140 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 708 ASN A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 13908 Z= 0.307 Angle : 0.693 10.494 19030 Z= 0.357 Chirality : 0.043 0.174 2094 Planarity : 0.005 0.055 2220 Dihedral : 17.765 176.327 2420 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1512 helix: 1.45 (0.20), residues: 654 sheet: -1.23 (0.44), residues: 152 loop : -1.82 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A1090 HIS 0.007 0.002 HIS A 795 PHE 0.011 0.002 PHE B1022 TYR 0.022 0.002 TYR A 907 ARG 0.009 0.001 ARG B 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2362 time to fit residues: 58.0692 Evaluate side-chains 100 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN B 555 ASN B 708 ASN B 782 ASN ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13908 Z= 0.207 Angle : 0.551 6.988 19030 Z= 0.288 Chirality : 0.039 0.187 2094 Planarity : 0.004 0.043 2220 Dihedral : 17.785 176.712 2420 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.23 % Allowed : 2.18 % Favored : 97.59 % 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: 0.01 (0.23), residues: 1512 helix: 1.89 (0.21), residues: 642 sheet: -0.67 (0.50), residues: 134 loop : -1.67 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1090 HIS 0.003 0.001 HIS B 559 PHE 0.018 0.001 PHE B1054 TYR 0.010 0.001 TYR B 907 ARG 0.004 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.2269 time to fit residues: 52.7882 Evaluate side-chains 101 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN B 708 ASN B 795 HIS ** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13908 Z= 0.188 Angle : 0.533 6.876 19030 Z= 0.280 Chirality : 0.038 0.135 2094 Planarity : 0.003 0.037 2220 Dihedral : 17.865 176.561 2420 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.08 % Allowed : 1.20 % Favored : 98.72 % 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: 0.21 (0.23), residues: 1512 helix: 2.06 (0.21), residues: 644 sheet: -0.79 (0.49), residues: 138 loop : -1.52 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1090 HIS 0.003 0.001 HIS A 559 PHE 0.006 0.001 PHE B 867 TYR 0.022 0.001 TYR A1030 ARG 0.003 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.2479 time to fit residues: 55.2491 Evaluate side-chains 96 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 961 HIS A1095 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 HIS B1095 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13908 Z= 0.152 Angle : 0.513 6.963 19030 Z= 0.266 Chirality : 0.038 0.124 2094 Planarity : 0.003 0.036 2220 Dihedral : 17.868 178.245 2420 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 0.33 (0.23), residues: 1512 helix: 2.06 (0.21), residues: 650 sheet: -0.77 (0.49), residues: 140 loop : -1.36 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1090 HIS 0.002 0.001 HIS A 795 PHE 0.016 0.001 PHE B1054 TYR 0.017 0.001 TYR B1030 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2377 time to fit residues: 56.2354 Evaluate side-chains 102 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 84 optimal weight: 0.0060 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 0.0020 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS B1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13908 Z= 0.128 Angle : 0.512 8.214 19030 Z= 0.258 Chirality : 0.037 0.128 2094 Planarity : 0.003 0.034 2220 Dihedral : 17.779 179.346 2420 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1512 helix: 2.00 (0.21), residues: 658 sheet: -0.66 (0.50), residues: 134 loop : -1.27 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 664 HIS 0.003 0.001 HIS A 548 PHE 0.005 0.001 PHE B 895 TYR 0.015 0.001 TYR B1030 ARG 0.002 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2388 time to fit residues: 57.4309 Evaluate side-chains 107 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1095 GLN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13908 Z= 0.165 Angle : 0.527 6.769 19030 Z= 0.271 Chirality : 0.038 0.145 2094 Planarity : 0.003 0.032 2220 Dihedral : 17.860 178.534 2420 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1512 helix: 2.08 (0.21), residues: 662 sheet: -0.87 (0.49), residues: 134 loop : -1.34 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1090 HIS 0.003 0.001 HIS B 795 PHE 0.016 0.001 PHE B1054 TYR 0.013 0.001 TYR A 907 ARG 0.003 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2460 time to fit residues: 52.6904 Evaluate side-chains 86 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 92 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13908 Z= 0.166 Angle : 0.531 6.736 19030 Z= 0.271 Chirality : 0.038 0.143 2094 Planarity : 0.003 0.034 2220 Dihedral : 17.970 179.873 2420 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1512 helix: 2.03 (0.21), residues: 662 sheet: -0.99 (0.48), residues: 134 loop : -1.35 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 664 HIS 0.004 0.001 HIS A 548 PHE 0.009 0.001 PHE A 867 TYR 0.012 0.001 TYR B 757 ARG 0.011 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2252 time to fit residues: 46.5408 Evaluate side-chains 89 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS B1095 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13908 Z= 0.185 Angle : 0.556 7.805 19030 Z= 0.284 Chirality : 0.038 0.140 2094 Planarity : 0.003 0.032 2220 Dihedral : 18.061 179.174 2420 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % 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: 0.31 (0.23), residues: 1512 helix: 2.04 (0.21), residues: 662 sheet: -1.08 (0.47), residues: 134 loop : -1.37 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1090 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.001 PHE B1054 TYR 0.015 0.001 TYR A1030 ARG 0.003 0.000 ARG B 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2320 time to fit residues: 47.7020 Evaluate side-chains 93 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 127 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1095 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061476 restraints weight = 57079.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063713 restraints weight = 32462.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065320 restraints weight = 21509.144| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13908 Z= 0.138 Angle : 0.545 9.166 19030 Z= 0.275 Chirality : 0.038 0.152 2094 Planarity : 0.003 0.033 2220 Dihedral : 17.981 179.899 2420 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1512 helix: 2.06 (0.21), residues: 660 sheet: -0.89 (0.48), residues: 134 loop : -1.31 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 664 HIS 0.003 0.001 HIS B 548 PHE 0.008 0.001 PHE A 569 TYR 0.025 0.001 TYR A1030 ARG 0.005 0.000 ARG A 804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.88 seconds wall clock time: 47 minutes 31.55 seconds (2851.55 seconds total)