Starting phenix.real_space_refine on Fri Mar 22 10:17:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/03_2024/5w9j_8785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/03_2024/5w9j_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_8785/03_2024/5w9j_8785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/03_2024/5w9j_8785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/03_2024/5w9j_8785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9j_8785/03_2024/5w9j_8785.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-5265/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: 16.94, per 1000 atoms: 0.51 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: 11.67 Conformation dependent library (CDL) restraints added in 5.5 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: 3.63 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: 13.94 Time building geometry restraints manager: 12.86 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. 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.380 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 82.630 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 1.569 12.380 45876 Z= 1.047 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 : 5.79 Ramachandran Plot: Outliers : 1.21 % Allowed : 3.97 % Favored : 94.82 % Rotamer: Outliers : 0.90 % Allowed : 1.56 % Favored : 97.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP G1184 HIS 0.009 0.001 HIS L 194 PHE 0.035 0.004 PHE F 71 TYR 0.046 0.006 TYR L 438 ARG 0.006 0.001 ARG D 979 *********************** 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 : 0.402 Fit side-chains revert: symmetry clash REVERT: A 906 MET cc_start: 0.2268 (ttt) cc_final: 0.1933 (mmt) REVERT: A 909 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4110 (p90) REVERT: A 1012 PHE cc_start: 0.8682 (m-80) cc_final: 0.7837 (m-10) REVERT: A 1134 LEU cc_start: 0.9408 (mt) cc_final: 0.8758 (pt) REVERT: A 1138 HIS cc_start: 0.8592 (m-70) cc_final: 0.7745 (m170) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.1519 time to fit residues: 11.6042 Evaluate side-chains 25 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.411 Evaluate side-chains 22 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.101 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: 0.1857 time to fit residues: 4.4393 Evaluate side-chains 13 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.114 Evaluate side-chains 33 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 GLU cc_start: 0.7796 (tp30) cc_final: 0.7207 (mp0) REVERT: C 70 ASP cc_start: 0.8346 (t0) cc_final: 0.7605 (m-30) REVERT: C 87 PHE cc_start: 0.8672 (m-80) cc_final: 0.8239 (m-80) REVERT: C 90 GLN cc_start: 0.8327 (tp40) cc_final: 0.7800 (pp30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1533 time to fit residues: 5.4511 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.107 Evaluate side-chains 81 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: J 169 LEU cc_start: 0.9112 (tp) cc_final: 0.8822 (tp) REVERT: J 218 ASN cc_start: 0.8593 (t0) cc_final: 0.7916 (p0) REVERT: J 277 ASN cc_start: 0.9161 (m110) cc_final: 0.8750 (m110) REVERT: J 288 ASP cc_start: 0.7579 (m-30) cc_final: 0.6859 (t0) REVERT: J 511 ARG cc_start: 0.3261 (mtm-85) cc_final: 0.2770 (ttt180) REVERT: J 593 ASP cc_start: 0.6622 (t0) cc_final: 0.6349 (m-30) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1719 time to fit residues: 18.6710 Evaluate side-chains 42 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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: 0.4980 chunk 200 optimal weight: 9.9990 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... 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 618 GLN K 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33735 Z= 0.229 Angle : 0.701 8.505 45876 Z= 0.389 Chirality : 0.045 0.178 5091 Planarity : 0.007 0.094 5961 Dihedral : 5.964 31.933 4629 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.33 % Favored : 95.10 % Rotamer: Outliers : 0.33 % Allowed : 1.40 % Favored : 98.28 % 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: 0.35 (0.13), residues: 4227 helix: 0.86 (0.19), residues: 714 sheet: 0.16 (0.15), residues: 1005 loop : 0.19 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 47 HIS 0.007 0.001 HIS K 681 PHE 0.020 0.002 PHE F 87 TYR 0.030 0.002 TYR D 777 ARG 0.008 0.000 ARG I 96 *********************** 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 46 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.424 Fit side-chains REVERT: D 830 LYS cc_start: 0.9138 (mttt) cc_final: 0.8921 (mttt) REVERT: D 836 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8302 (t70) REVERT: D 925 CYS cc_start: 0.1455 (OUTLIER) cc_final: 0.1131 (p) REVERT: D 928 TYR cc_start: 0.6533 (p90) cc_final: 0.6016 (t80) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 0.0976 time to fit residues: 6.2012 Evaluate side-chains 25 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.404 Evaluate side-chains 18 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8368 (m-40) cc_final: 0.8138 (m110) REVERT: E 69 MET cc_start: 0.6826 (tpt) cc_final: 0.6545 (tpt) REVERT: E 80 MET cc_start: 0.8093 (tpp) cc_final: 0.7666 (ttm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1921 time to fit residues: 3.7840 Evaluate side-chains 13 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.119 Evaluate side-chains 25 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8675 (mt) cc_final: 0.8426 (mt) REVERT: F 70 ASP cc_start: 0.8433 (t0) cc_final: 0.7812 (m-30) REVERT: F 90 GLN cc_start: 0.8073 (tp40) cc_final: 0.7768 (pp30) REVERT: F 104 LEU cc_start: 0.8454 (mt) cc_final: 0.8061 (tp) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1394 time to fit residues: 3.8158 Evaluate side-chains 17 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.103 Evaluate side-chains 52 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: K 116 PHE cc_start: 0.8435 (p90) cc_final: 0.8005 (p90) REVERT: K 225 LEU cc_start: 0.9273 (tp) cc_final: 0.8833 (mt) REVERT: K 277 ASN cc_start: 0.8510 (m110) cc_final: 0.8152 (m110) REVERT: K 288 ASP cc_start: 0.7730 (m-30) cc_final: 0.7066 (t0) REVERT: K 452 MET cc_start: 0.4284 (ttm) cc_final: 0.4036 (ptm) REVERT: K 511 ARG cc_start: 0.3041 (mtm-85) cc_final: 0.2693 (ttt180) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1754 time to fit residues: 12.8786 Evaluate side-chains 38 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 7.9990 chunk 118 optimal weight: 30.0000 chunk 317 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 105 optimal weight: 0.2980 chunk 382 optimal weight: 9.9990 chunk 412 optimal weight: 0.8980 chunk 340 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 306 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1097 GLN 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: H 3 GLN H 6 GLN 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: C 76 HIS ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33735 Z= 0.302 Angle : 0.957 24.484 45876 Z= 0.499 Chirality : 0.064 1.354 5091 Planarity : 0.009 0.128 5961 Dihedral : 6.151 31.170 4629 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.18 % Favored : 94.39 % Rotamer: Outliers : 0.66 % Allowed : 1.97 % Favored : 97.37 % 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: -0.14 (0.12), residues: 4227 helix: 0.31 (0.19), residues: 690 sheet: -0.15 (0.15), residues: 978 loop : -0.08 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP I 35 HIS 0.018 0.003 HIS A 836 PHE 0.128 0.004 PHE D 895 TYR 0.126 0.004 TYR D1141 ARG 0.058 0.002 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 3 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 40 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 906 MET cc_start: -0.0512 (OUTLIER) cc_final: -0.1804 (pmm) REVERT: D 925 CYS cc_start: 0.2161 (OUTLIER) cc_final: 0.1718 (p) REVERT: D 928 TYR cc_start: 0.6635 (p90) cc_final: 0.6129 (t80) outliers start: 6 outliers final: 1 residues processed: 38 average time/residue: 0.1249 time to fit residues: 6.4408 Evaluate side-chains 29 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.410 Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.8099 (tpp) cc_final: 0.7544 (ttm) REVERT: H 100 MET cc_start: 0.7587 (tpp) cc_final: 0.7276 (tpp) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.1713 time to fit residues: 3.0422 Evaluate side-chains 11 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.122 Evaluate side-chains 24 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 ASP cc_start: 0.8372 (t0) cc_final: 0.7686 (m-30) REVERT: C 73 LEU cc_start: 0.8789 (tp) cc_final: 0.8572 (tp) REVERT: C 104 LEU cc_start: 0.8242 (mt) cc_final: 0.7854 (tp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1351 time to fit residues: 3.5590 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.089 Evaluate side-chains 45 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 225 LEU cc_start: 0.9267 (tp) cc_final: 0.8816 (mt) REVERT: K 277 ASN cc_start: 0.8473 (m110) cc_final: 0.8068 (m110) REVERT: K 278 MET cc_start: 0.8131 (tpp) cc_final: 0.7920 (tpp) REVERT: K 288 ASP cc_start: 0.7732 (m-30) cc_final: 0.7066 (t0) REVERT: K 511 ARG cc_start: 0.3064 (mtm-85) cc_final: 0.2717 (ttt180) REVERT: K 589 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8117 (mm-30) REVERT: K 696 MET cc_start: 0.5437 (pmm) cc_final: 0.5150 (pmm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1400 time to fit residues: 9.2191 Evaluate side-chains 36 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 7.9990 chunk 287 optimal weight: 0.0050 chunk 198 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 383 optimal weight: 0.2980 chunk 405 optimal weight: 5.9990 chunk 200 optimal weight: 0.0070 chunk 363 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 overall best weight: 0.3012 ------------------------------------------------------------------------------- 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** D1020 HIS D1031 GLN Total number of N/Q/H flips: 2 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 33735 Z= 0.303 Angle : 0.889 15.396 45876 Z= 0.477 Chirality : 0.054 0.423 5091 Planarity : 0.009 0.138 5961 Dihedral : 6.073 31.301 4629 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.11 % Favored : 94.46 % Rotamer: Outliers : 0.41 % Allowed : 3.12 % Favored : 96.47 % Cbeta Deviations : 0.08 % 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: -0.34 (0.12), residues: 4227 helix: 0.13 (0.19), residues: 669 sheet: -0.23 (0.15), residues: 978 loop : -0.23 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 47 HIS 0.021 0.002 HIS G 836 PHE 0.062 0.004 PHE C 87 TYR 0.063 0.003 TYR D1171 ARG 0.046 0.002 ARG A1057 *********************** 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 35 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 928 TYR cc_start: 0.6700 (p90) cc_final: 0.6162 (t80) REVERT: D 1129 ASN cc_start: 0.8778 (m-40) cc_final: 0.8531 (m-40) outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1138 time to fit residues: 5.6598 Evaluate side-chains 26 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.433 Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8324 (m-40) cc_final: 0.8093 (m110) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2213 time to fit residues: 3.6280 Evaluate side-chains 9 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.128 Evaluate side-chains 22 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8499 (mt) cc_final: 0.8062 (mt) REVERT: F 27 GLU cc_start: 0.8396 (tp30) cc_final: 0.7832 (tm-30) REVERT: F 70 ASP cc_start: 0.8419 (t0) cc_final: 0.7869 (m-30) REVERT: F 73 LEU cc_start: 0.8969 (tp) cc_final: 0.8767 (tp) REVERT: F 104 LEU cc_start: 0.8400 (mt) cc_final: 0.8007 (tp) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.1130 time to fit residues: 2.7192 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.103 Evaluate side-chains 46 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: K 288 ASP cc_start: 0.7730 (m-30) cc_final: 0.6945 (t0) REVERT: K 289 THR cc_start: 0.7407 (m) cc_final: 0.6952 (p) REVERT: K 511 ARG cc_start: 0.3207 (mtm-85) cc_final: 0.2789 (ttt180) REVERT: K 589 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8132 (mm-30) REVERT: K 717 LEU cc_start: 0.7828 (mt) cc_final: 0.7304 (tp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1528 time to fit residues: 10.4798 Evaluate side-chains 39 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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: 51.9358 > 50: distance: 0 - 1: 6.793 distance: 1 - 2: 6.929 distance: 1 - 4: 5.271 distance: 2 - 3: 11.094 distance: 2 - 7: 17.251 distance: 4 - 5: 3.737 distance: 7 - 8: 29.852 distance: 8 - 9: 20.224 distance: 8 - 11: 28.105 distance: 9 - 10: 12.600 distance: 9 - 14: 8.631 distance: 11 - 12: 51.936 distance: 11 - 13: 16.873 distance: 14 - 15: 7.365 distance: 15 - 16: 9.348 distance: 15 - 18: 17.750 distance: 16 - 17: 11.242 distance: 16 - 21: 14.839 distance: 18 - 19: 14.807 distance: 18 - 20: 15.266 distance: 21 - 22: 18.260 distance: 22 - 23: 17.004 distance: 22 - 25: 5.661 distance: 23 - 24: 14.246 distance: 23 - 29: 11.290 distance: 25 - 26: 3.949 distance: 26 - 27: 4.554 distance: 26 - 28: 4.476 distance: 29 - 30: 9.318 distance: 30 - 31: 8.323 distance: 30 - 33: 6.257 distance: 31 - 32: 3.070 distance: 31 - 35: 7.988 distance: 35 - 36: 7.705 distance: 36 - 37: 8.451 distance: 36 - 39: 22.206 distance: 37 - 38: 6.400 distance: 37 - 44: 8.643 distance: 39 - 40: 43.168 distance: 40 - 41: 20.546 distance: 44 - 45: 9.845 distance: 45 - 46: 15.838 distance: 45 - 48: 22.703 distance: 46 - 47: 38.226 distance: 46 - 53: 25.481 distance: 48 - 49: 15.785 distance: 49 - 50: 17.006 distance: 50 - 51: 7.433 distance: 50 - 52: 12.890 distance: 53 - 54: 14.608 distance: 54 - 55: 17.070 distance: 54 - 57: 19.899 distance: 55 - 56: 23.918 distance: 55 - 65: 30.919 distance: 57 - 58: 31.675 distance: 58 - 59: 12.321 distance: 58 - 60: 13.622 distance: 59 - 61: 17.017 distance: 60 - 62: 28.571 distance: 61 - 63: 15.231 distance: 62 - 63: 18.225 distance: 63 - 64: 6.569 distance: 65 - 66: 17.146 distance: 66 - 67: 10.292 distance: 66 - 69: 20.435 distance: 67 - 68: 14.462 distance: 67 - 72: 11.619 distance: 69 - 70: 23.693 distance: 69 - 71: 16.622 distance: 72 - 73: 10.075 distance: 73 - 74: 5.617 distance: 73 - 76: 5.026 distance: 74 - 75: 6.183