Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:35:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/12_2022/5w9j_8785.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F GLU 27": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32958 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "K" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "L" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 17.44, per 1000 atoms: 0.53 Number of scatterers: 32958 At special positions: 0 Unit cell: (155.04, 154.02, 191.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6399 8.00 N 5475 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.09 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.12 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.09 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.12 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.09 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.12 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.10 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.07 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.83 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.04 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.09 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.21 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.28 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.02 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.09 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.10 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.07 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.84 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.03 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.04 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.09 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.21 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.28 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=2.02 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=2.09 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.10 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.07 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.84 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.03 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.04 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=2.09 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=2.22 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=2.28 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=2.02 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.09 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: 13.36 Conformation dependent library (CDL) restraints added in 5.1 seconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 75 sheets defined 22.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.832A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 908 through 913 Processing helix chain 'D' and resid 926 through 931 removed outlier: 3.627A pdb=" N ALA D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 984 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1011 Processing helix chain 'D' and resid 1016 through 1040 removed outlier: 3.551A pdb=" N LEU D1033 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D1040 " --> pdb=" O LEU D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1057 Processing helix chain 'D' and resid 1059 through 1107 Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.991A pdb=" N GLY E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.831A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.626A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.550A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.990A pdb=" N GLY B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'G' and resid 816 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.831A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 913 Processing helix chain 'G' and resid 926 through 931 removed outlier: 3.626A pdb=" N ALA G 930 " --> pdb=" O ALA G 926 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 984 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1011 Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.550A pdb=" N LEU G1033 " --> pdb=" O ASN G1029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1057 Processing helix chain 'G' and resid 1059 through 1107 Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.991A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.868A pdb=" N ASP J 41 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.628A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 416 removed outlier: 3.647A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 436 Processing helix chain 'J' and resid 451 through 455 removed outlier: 3.734A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 676 through 678 No H-bonds generated for 'chain 'J' and resid 676 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.868A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 107 Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 303 through 307 Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.629A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.647A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 451 through 455 removed outlier: 3.733A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 676 through 678 No H-bonds generated for 'chain 'K' and resid 676 through 678' Processing helix chain 'K' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.869A pdb=" N ASP L 41 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 107 Processing helix chain 'L' and resid 133 through 137 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 303 through 307 Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 390 removed outlier: 3.629A pdb=" N SER L 390 " --> pdb=" O PRO L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 416 removed outlier: 3.648A pdb=" N LEU L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 436 Processing helix chain 'L' and resid 451 through 455 removed outlier: 3.733A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 676 through 678 No H-bonds generated for 'chain 'L' and resid 676 through 678' Processing helix chain 'L' and resid 694 through 702 removed outlier: 5.117A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 717 through 724 removed outlier: 7.025A pdb=" N MET D 757 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER J 720 " --> pdb=" O MET D 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU D 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU J 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 737 " --> pdb=" O LEU J 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU J 729 " --> pdb=" O ALA J 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.820A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'D' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'D' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.513A pdb=" N VAL E 16 " --> pdb=" O ARG E 82B" (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG E 82B" --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.061A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 717 through 724 removed outlier: 7.024A pdb=" N MET A 757 " --> pdb=" O VAL K 718 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER K 720 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 737 " --> pdb=" O LEU K 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU K 729 " --> pdb=" O ALA K 737 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.514A pdb=" N VAL B 16 " --> pdb=" O ARG B 82B" (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B 82B" --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 33 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA B 33 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.061A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 717 through 724 removed outlier: 7.024A pdb=" N MET G 757 " --> pdb=" O VAL L 718 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER L 720 " --> pdb=" O MET G 757 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA L 737 " --> pdb=" O LEU L 729 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU L 729 " --> pdb=" O ALA L 737 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.882A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 3.619A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.514A pdb=" N VAL H 16 " --> pdb=" O ARG H 82B" (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG H 82B" --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA H 33 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.448A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA H 33 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 7.060A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.687A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.340A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'J' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 180 " --> pdb=" O THR J 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR J 242 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA J 182 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET J 240 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR J 184 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 186 " --> pdb=" O ASN J 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN J 236 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU J 188 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU J 234 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.582A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY J 675 " --> pdb=" O PRO J 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 374 through 375 Processing sheet with id=AE8, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.313A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.560A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.471A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 617 through 619 removed outlier: 6.100A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AF4, first strand: chain 'K' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 83 through 85 removed outlier: 3.687A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.341A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AF8, first strand: chain 'K' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU K 180 " --> pdb=" O THR K 242 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR K 242 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA K 182 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET K 240 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR K 184 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 186 " --> pdb=" O ASN K 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN K 236 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU K 188 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU K 234 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG2, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.581A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY K 675 " --> pdb=" O PRO K 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS K 713 " --> pdb=" O PHE K 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG4, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.313A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.562A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR K 483 " --> pdb=" O VAL K 420 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL K 420 " --> pdb=" O THR K 483 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.472A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 617 through 619 removed outlier: 6.100A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AG9, first strand: chain 'L' and resid 68 through 76 removed outlier: 6.539A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 83 through 85 removed outlier: 3.686A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 88 through 89 removed outlier: 7.340A pdb=" N SER L 88 " --> pdb=" O ILE L 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH4, first strand: chain 'L' and resid 109 through 111 removed outlier: 4.600A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU L 180 " --> pdb=" O THR L 242 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR L 242 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA L 182 " --> pdb=" O MET L 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET L 240 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR L 184 " --> pdb=" O THR L 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 186 " --> pdb=" O ASN L 236 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN L 236 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU L 188 " --> pdb=" O LEU L 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU L 234 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 126 through 127 removed outlier: 3.684A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.583A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY L 675 " --> pdb=" O PRO L 658 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS L 713 " --> pdb=" O PHE L 674 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 374 through 375 Processing sheet with id=AH9, first strand: chain 'L' and resid 381 through 382 removed outlier: 6.312A pdb=" N VAL L 381 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS L 407 " --> pdb=" O CYS L 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'L' and resid 400 through 404 removed outlier: 3.561A pdb=" N LYS L 400 " --> pdb=" O TYR L 445 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR L 483 " --> pdb=" O VAL L 420 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL L 420 " --> pdb=" O THR L 483 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.471A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 617 through 619 removed outlier: 6.101A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3534 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: 15.33 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 5445 1.30 - 1.43: 9453 1.43 - 1.57: 18588 1.57 - 1.70: 3 1.70 - 1.84: 246 Bond restraints: 33735 Sorted by residual: bond pdb=" CA ASN K 236 " pdb=" C ASN K 236 " ideal model delta sigma weight residual 1.531 1.451 0.081 1.08e-02 8.57e+03 5.59e+01 bond pdb=" CA ASN L 236 " pdb=" C ASN L 236 " ideal model delta sigma weight residual 1.531 1.451 0.080 1.08e-02 8.57e+03 5.55e+01 bond pdb=" CA ASN J 236 " pdb=" C ASN J 236 " ideal model delta sigma weight residual 1.531 1.452 0.080 1.08e-02 8.57e+03 5.46e+01 bond pdb=" C CYS K 383 " pdb=" O CYS K 383 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.14e-02 7.69e+03 3.98e+01 bond pdb=" C CYS L 383 " pdb=" O CYS L 383 " ideal model delta sigma weight residual 1.234 1.162 0.071 1.14e-02 7.69e+03 3.90e+01 ... (remaining 33730 not shown) Histogram of bond angle deviations from ideal: 94.01 - 101.98: 96 101.98 - 109.94: 7729 109.94 - 117.91: 17810 117.91 - 125.87: 19876 125.87 - 133.84: 365 Bond angle restraints: 45876 Sorted by residual: angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 120.21 129.96 -9.75 9.60e-01 1.09e+00 1.03e+02 angle pdb=" C VAL I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta sigma weight residual 120.21 129.92 -9.71 9.60e-01 1.09e+00 1.02e+02 angle pdb=" C VAL F 58 " pdb=" N PRO F 59 " pdb=" CA PRO F 59 " ideal model delta sigma weight residual 120.21 129.92 -9.71 9.60e-01 1.09e+00 1.02e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 126.82 -7.16 7.20e-01 1.93e+00 9.88e+01 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.80 -7.14 7.20e-01 1.93e+00 9.84e+01 ... (remaining 45871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 19016 17.24 - 34.47: 791 34.47 - 51.71: 192 51.71 - 68.94: 113 68.94 - 86.18: 27 Dihedral angle restraints: 20139 sinusoidal: 7749 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS A1106 " pdb=" SG CYS A1106 " pdb=" SG CYS A1117 " pdb=" CB CYS A1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.86 -82.86 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.85 -82.85 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS G1106 " pdb=" SG CYS G1106 " pdb=" SG CYS G1117 " pdb=" CB CYS G1117 " ideal model delta sinusoidal sigma weight residual 93.00 175.85 -82.85 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 20136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3437 0.075 - 0.150: 1440 0.150 - 0.225: 190 0.225 - 0.300: 18 0.300 - 0.375: 6 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CA CYS L 727 " pdb=" N CYS L 727 " pdb=" C CYS L 727 " pdb=" CB CYS L 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA CYS J 727 " pdb=" N CYS J 727 " pdb=" C CYS J 727 " pdb=" CB CYS J 727 " 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 CYS K 727 " pdb=" N CYS K 727 " pdb=" C CYS K 727 " pdb=" CB CYS K 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 5088 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO D1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO D1219 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO D1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO A1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO A1219 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO A1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G1218 " 0.105 5.00e-02 4.00e+02 1.60e-01 4.10e+01 pdb=" N PRO G1219 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO G1219 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO G1219 " 0.083 5.00e-02 4.00e+02 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 96 2.48 - 3.09: 25784 3.09 - 3.69: 51279 3.69 - 4.30: 80500 4.30 - 4.90: 123352 Nonbonded interactions: 281011 Sorted by model distance: nonbonded pdb=" CE2 PHE J 506 " pdb=" CG2 VAL J 555 " model vdw 1.881 3.760 nonbonded pdb=" CE1 PHE J 506 " pdb=" OE1 GLU J 513 " model vdw 1.882 3.340 nonbonded pdb=" CE1 PHE L 506 " pdb=" OE1 GLU L 513 " model vdw 1.883 3.340 nonbonded pdb=" CE1 PHE K 506 " pdb=" OE1 GLU K 513 " model vdw 1.883 3.340 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.928 3.760 ... (remaining 281006 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 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20904 2.51 5 N 5475 2.21 5 O 6399 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.080 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: 0.030 Extract box with map and model: 8.880 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 85.930 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.013 0.082 33735 Z= 0.878 Angle : 1.568 12.380 45876 Z= 1.045 Chirality : 0.075 0.375 5091 Planarity : 0.017 0.160 5961 Dihedral : 11.982 86.176 12066 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 1.21 % Allowed : 3.97 % Favored : 94.82 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % 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: 0.53 (0.12), residues: 4227 helix: 0.52 (0.19), residues: 726 sheet: 0.02 (0.15), residues: 978 loop : 0.61 (0.12), residues: 2523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.1544 time to fit residues: 11.8221 Evaluate side-chains 23 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5267 Evaluate side-chains 22 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.104 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: 1 residues processed: 22 average time/residue: 0.1778 time to fit residues: 4.2574 Evaluate side-chains 13 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0275 time to fit residues: 0.1951 Evaluate side-chains 33 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1542 time to fit residues: 5.4977 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1429 Evaluate side-chains 81 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.716 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1702 time to fit residues: 18.4048 Evaluate side-chains 39 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.0517 time to fit residues: 1.1829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 chunk 176 optimal weight: 0.4980 chunk 108 optimal weight: 0.4980 chunk 214 optimal weight: 0.0770 chunk 170 optimal weight: 6.9990 chunk 329 optimal weight: 0.0570 chunk 127 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 381 optimal weight: 0.1980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 914 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 410 ASN K 618 GLN K 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 33735 Z= 0.247 Angle : 0.734 15.652 45876 Z= 0.397 Chirality : 0.045 0.178 5091 Planarity : 0.008 0.141 5961 Dihedral : 6.055 32.177 4629 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.33 % Favored : 95.10 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.30 (0.13), residues: 4227 helix: 0.81 (0.19), residues: 717 sheet: 0.18 (0.15), residues: 957 loop : 0.13 (0.12), residues: 2553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8446 Ramachandran restraints generated. 4223 Oldfield, 0 Emsley, 4223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8446 Ramachandran restraints generated. 4223 Oldfield, 0 Emsley, 4223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.427 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.1260 time to fit residues: 7.7122 Evaluate side-chains 28 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5716 Evaluate side-chains 19 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1867 time to fit residues: 3.8920 Evaluate side-chains 12 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1600 Evaluate side-chains 25 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.1701 time to fit residues: 4.5963 Evaluate side-chains 12 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.099 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3851 time to fit residues: 0.5240 Evaluate side-chains 51 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.718 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1549 time to fit residues: 11.2192 Evaluate side-chains 34 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 8.9990 chunk 118 optimal weight: 0.2980 chunk 317 optimal weight: 0.2980 chunk 259 optimal weight: 0.0000 chunk 105 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 412 optimal weight: 2.9990 chunk 340 optimal weight: 0.6980 chunk 378 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1097 GLN ** D1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1145 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 33735 Z= 0.421 Angle : 1.067 26.717 45876 Z= 0.540 Chirality : 0.058 0.856 5091 Planarity : 0.009 0.107 5961 Dihedral : 6.192 31.170 4629 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.97 % Favored : 94.46 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.06 (0.12), residues: 4227 helix: 0.51 (0.19), residues: 690 sheet: -0.12 (0.15), residues: 939 loop : -0.07 (0.12), residues: 2598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1115 time to fit residues: 5.5820 Evaluate side-chains 22 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5717 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 0.1937 time to fit residues: 2.8013 Evaluate side-chains 10 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1511 Evaluate side-chains 21 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1616 time to fit residues: 3.7278 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1361 Evaluate side-chains 40 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1528 time to fit residues: 8.9987 Evaluate side-chains 32 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 182 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 363 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1079 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 33735 Z= 0.421 Angle : 1.067 26.711 45876 Z= 0.540 Chirality : 0.058 0.856 5091 Planarity : 0.009 0.107 5961 Dihedral : 6.192 31.170 4629 Min Nonbonded Distance : 0.768 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.97 % Favored : 94.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.06 (0.12), residues: 4227 helix: 0.51 (0.19), residues: 690 sheet: -0.12 (0.15), residues: 939 loop : -0.07 (0.12), residues: 2598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.425 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0997 time to fit residues: 3.4690 Evaluate side-chains 20 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5509 Evaluate side-chains 12 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1981 time to fit residues: 2.6605 Evaluate side-chains 10 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1584 Evaluate side-chains 17 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0936 time to fit residues: 1.8788 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1341 Evaluate side-chains 40 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1296 time to fit residues: 8.0207 Evaluate side-chains 31 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 20.0000 chunk 230 optimal weight: 0.0470 chunk 5 optimal weight: 0.0000 chunk 302 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 346 optimal weight: 0.1980 chunk 280 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 364 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1129 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 33735 Z= 0.264 Angle : 0.823 13.804 45876 Z= 0.439 Chirality : 0.052 0.422 5091 Planarity : 0.009 0.150 5961 Dihedral : 6.131 32.691 4629 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.25 % Favored : 94.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.12), residues: 4227 helix: 0.15 (0.19), residues: 690 sheet: -0.41 (0.15), residues: 954 loop : -0.21 (0.12), residues: 2583 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0973 time to fit residues: 4.0520 Evaluate side-chains 19 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5529 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.2133 time to fit residues: 3.2629 Evaluate side-chains 9 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1460 Evaluate side-chains 17 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0687 time to fit residues: 1.4531 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1343 Evaluate side-chains 42 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1320 time to fit residues: 8.4271 Evaluate side-chains 34 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.3892 > 50: distance: 0 - 2: 16.145 distance: 1 - 2: 15.531 distance: 3 - 4: 4.989 distance: 4 - 5: 11.765 distance: 4 - 7: 29.874 distance: 5 - 6: 32.574 distance: 5 - 11: 12.470 distance: 7 - 8: 7.369 distance: 8 - 9: 33.774 distance: 9 - 10: 20.998 distance: 11 - 12: 12.320 distance: 12 - 13: 6.755 distance: 12 - 15: 19.621 distance: 13 - 14: 8.935 distance: 13 - 19: 20.215 distance: 15 - 16: 30.251 distance: 16 - 17: 11.969 distance: 16 - 18: 15.931 distance: 19 - 20: 9.753 distance: 20 - 21: 19.295 distance: 20 - 23: 9.022 distance: 21 - 22: 7.010 distance: 21 - 33: 11.503 distance: 23 - 24: 8.251 distance: 24 - 25: 9.915 distance: 24 - 26: 8.046 distance: 25 - 27: 5.901 distance: 26 - 28: 9.690 distance: 26 - 29: 5.905 distance: 27 - 28: 6.529 distance: 28 - 30: 5.066 distance: 29 - 31: 12.187 distance: 30 - 32: 8.864 distance: 31 - 32: 11.502 distance: 33 - 34: 15.218 distance: 34 - 35: 10.134 distance: 34 - 37: 10.287 distance: 35 - 36: 16.625 distance: 35 - 44: 17.286 distance: 37 - 38: 9.961 distance: 38 - 39: 9.991 distance: 38 - 40: 9.837 distance: 39 - 41: 10.167 distance: 40 - 42: 13.991 distance: 41 - 43: 3.704 distance: 42 - 43: 19.636 distance: 44 - 45: 20.922 distance: 45 - 46: 15.705 distance: 45 - 48: 28.878 distance: 46 - 47: 10.493 distance: 46 - 53: 30.106 distance: 48 - 49: 22.153 distance: 49 - 50: 24.034 distance: 50 - 51: 6.755 distance: 50 - 52: 15.007 distance: 53 - 54: 29.916 distance: 54 - 55: 9.812 distance: 54 - 57: 9.144 distance: 55 - 56: 20.650 distance: 55 - 62: 18.833 distance: 57 - 58: 15.293 distance: 58 - 59: 38.994 distance: 59 - 60: 20.298 distance: 59 - 61: 33.958 distance: 62 - 63: 5.555 distance: 63 - 64: 5.772 distance: 63 - 66: 9.162 distance: 64 - 65: 6.720 distance: 64 - 71: 6.100 distance: 66 - 67: 28.977 distance: 67 - 68: 31.427 distance: 69 - 70: 36.935 distance: 71 - 72: 21.815 distance: 71 - 77: 14.120 distance: 72 - 73: 28.094 distance: 72 - 75: 4.918 distance: 73 - 74: 32.563 distance: 73 - 78: 25.225 distance: 75 - 76: 15.542 distance: 76 - 77: 12.583 distance: 78 - 79: 7.662 distance: 79 - 80: 14.105 distance: 80 - 81: 3.823 distance: 80 - 82: 6.625 distance: 82 - 83: 4.854 distance: 83 - 84: 9.810 distance: 83 - 86: 10.771 distance: 84 - 85: 6.597 distance: 84 - 91: 12.869 distance: 86 - 87: 14.566 distance: 87 - 88: 12.502 distance: 88 - 89: 6.720 distance: 91 - 92: 33.582