Starting phenix.real_space_refine on Fri May 30 06:42:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_8785.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_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/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_8785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_8785.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_8785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9j_8785/05_2025/5w9j_8785.cif" } 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. Time to flip 3 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 17.94, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 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: 8.31 Conformation dependent library (CDL) restraints added in 4.3 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: 5.55 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: 17.73 Time building geometry restraints manager: 9.65 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: 0.00 - 2.48: 41588 2.48 - 4.95: 3612 4.95 - 7.43: 527 7.43 - 9.90: 133 9.90 - 12.38: 16 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 Time spend for trying shortcut: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } 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 'K' selection = chain 'J' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 77.800 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.620 ------------------------------------------------------------------------------- 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 : 0.016 0.806 33792 Z= 0.959 Angle : 1.577 12.380 45990 Z= 1.049 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 Details of bonding type rmsd hydrogen bonds : bond 0.15960 ( 1244) hydrogen bonds : angle 8.99853 ( 3534) SS BOND : bond 0.20103 ( 57) SS BOND : angle 3.57043 ( 114) covalent geometry : bond 0.01349 (33735) covalent geometry : angle 1.56938 (45876) *********************** 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 to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.368 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: 0.1478 time to fit residues: 11.2838 Evaluate side-chains 25 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.399 Evaluate side-chains 78 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: K 169 LEU cc_start: 0.9107 (tp) cc_final: 0.8839 (tp) REVERT: K 218 ASN cc_start: 0.8544 (t0) cc_final: 0.7807 (p0) REVERT: K 277 ASN cc_start: 0.9218 (m110) cc_final: 0.8655 (m110) REVERT: K 288 ASP cc_start: 0.7846 (m-30) cc_final: 0.7027 (t0) REVERT: K 455 ASP cc_start: 0.6204 (m-30) cc_final: 0.6002 (t0) REVERT: K 511 ARG cc_start: 0.3176 (mtm-85) cc_final: 0.2548 (ttt180) REVERT: K 593 ASP cc_start: 0.6484 (t0) cc_final: 0.6279 (m-30) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.1552 time to fit residues: 16.3522 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.634 Evaluate side-chains 33 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.088 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: 0.1437 time to fit residues: 5.1091 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.089 Evaluate side-chains 22 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.103 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: 0.1804 time to fit residues: 4.3051 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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: 0.9990 chunk 318 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 214 optimal weight: 30.0000 chunk 170 optimal weight: 0.0270 chunk 329 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 chunk 245 optimal weight: 0.0970 chunk 381 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 ASN K 618 GLN K 637 ASN Total number of N/Q/H flips: 3 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050498 restraints weight = 24048.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051737 restraints weight = 15264.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052427 restraints weight = 10734.441| |-----------------------------------------------------------------------------| r_work (final): 0.3080 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.056746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046428 restraints weight = 64506.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.047363 restraints weight = 43392.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.048077 restraints weight = 32044.780| |-----------------------------------------------------------------------------| r_work (final): 0.3381 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.060241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.054502 restraints weight = 6794.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.055192 restraints weight = 5175.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.055831 restraints weight = 4194.291| |-----------------------------------------------------------------------------| r_work (final): 0.3452 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044662 restraints weight = 9531.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045685 restraints weight = 6540.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046470 restraints weight = 4793.180| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33792 Z= 0.160 Angle : 0.715 10.793 45990 Z= 0.394 Chirality : 0.045 0.186 5091 Planarity : 0.008 0.095 5961 Dihedral : 5.920 32.663 4629 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.47 % Favored : 95.03 % Rotamer: Outliers : 0.25 % Allowed : 1.81 % Favored : 97.95 % 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: 0.27 (0.12), residues: 4227 helix: 0.88 (0.19), residues: 696 sheet: 0.13 (0.15), residues: 969 loop : 0.10 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 47 HIS 0.007 0.001 HIS K 681 PHE 0.020 0.002 PHE I 87 TYR 0.028 0.002 TYR I 28 ARG 0.004 0.000 ARG L 181 Details of bonding type rmsd hydrogen bonds : bond 0.05569 ( 1244) hydrogen bonds : angle 6.90029 ( 3534) SS BOND : bond 0.00506 ( 57) SS BOND : angle 2.44221 ( 114) covalent geometry : bond 0.00347 (33735) covalent geometry : angle 0.70585 (45876) *********************** 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 to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: D 780 LEU cc_start: 0.9258 (tp) cc_final: 0.9048 (tt) REVERT: D 925 CYS cc_start: 0.1516 (OUTLIER) cc_final: 0.1110 (p) REVERT: D 928 TYR cc_start: 0.6276 (p90) cc_final: 0.5915 (t80) REVERT: D 1012 PHE cc_start: 0.8238 (m-80) cc_final: 0.8011 (m-80) REVERT: D 1134 LEU cc_start: 0.9256 (mt) cc_final: 0.9032 (mt) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.1298 time to fit residues: 8.1310 Evaluate side-chains 27 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.473 Evaluate side-chains 54 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: K 225 LEU cc_start: 0.8988 (tp) cc_final: 0.8560 (mt) REVERT: K 288 ASP cc_start: 0.7372 (m-30) cc_final: 0.6910 (t0) REVERT: K 511 ARG cc_start: 0.3067 (mtm-85) cc_final: 0.2627 (ttt180) REVERT: K 638 LEU cc_start: 0.8772 (tp) cc_final: 0.8527 (tp) REVERT: K 686 MET cc_start: 0.8058 (tpp) cc_final: 0.7535 (mmt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1825 time to fit residues: 14.2360 Evaluate side-chains 37 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.819 Evaluate side-chains 26 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 70 ASP cc_start: 0.7751 (t0) cc_final: 0.7117 (m-30) REVERT: F 90 GLN cc_start: 0.7426 (tp40) cc_final: 0.6819 (pp30) REVERT: F 104 LEU cc_start: 0.8534 (mt) cc_final: 0.8138 (tp) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1702 time to fit residues: 4.8230 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.102 Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8623 (m-40) cc_final: 0.8405 (m110) REVERT: E 69 MET cc_start: 0.6750 (tpt) cc_final: 0.6242 (mmm) REVERT: E 105 GLN cc_start: 0.8239 (pm20) cc_final: 0.7939 (pm20) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1898 time to fit residues: 4.1610 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4913 > 50: distance: 0 - 1: 16.926 distance: 0 - 3: 14.901 distance: 1 - 2: 22.778 distance: 1 - 7: 26.842 distance: 3 - 4: 14.108 distance: 3 - 5: 6.403 distance: 4 - 6: 19.618 distance: 7 - 8: 12.202 distance: 7 - 13: 24.474 distance: 8 - 9: 10.531 distance: 8 - 11: 30.861 distance: 9 - 10: 16.150 distance: 9 - 14: 37.431 distance: 10 - 39: 37.343 distance: 11 - 12: 16.637 distance: 12 - 13: 24.896 distance: 14 - 15: 16.440 distance: 15 - 16: 33.410 distance: 15 - 18: 37.503 distance: 16 - 17: 47.475 distance: 16 - 25: 29.672 distance: 17 - 45: 43.428 distance: 18 - 19: 11.434 distance: 19 - 20: 20.749 distance: 19 - 21: 17.472 distance: 20 - 22: 16.986 distance: 21 - 23: 12.362 distance: 22 - 24: 5.250 distance: 23 - 24: 6.554 distance: 25 - 26: 19.979 distance: 26 - 27: 40.738 distance: 26 - 29: 39.342 distance: 27 - 28: 33.062 distance: 27 - 30: 38.613 distance: 28 - 53: 17.899 distance: 30 - 31: 50.571 distance: 31 - 32: 23.099 distance: 31 - 34: 37.378 distance: 32 - 33: 35.645 distance: 32 - 39: 25.734 distance: 33 - 64: 34.808 distance: 34 - 35: 32.148 distance: 35 - 36: 9.157 distance: 36 - 37: 14.017 distance: 36 - 38: 43.721 distance: 39 - 40: 20.796 distance: 40 - 41: 36.978 distance: 40 - 43: 34.960 distance: 41 - 42: 46.512 distance: 42 - 76: 23.851 distance: 43 - 44: 40.813 distance: 46 - 47: 40.195 distance: 46 - 49: 52.755 distance: 47 - 48: 33.225 distance: 47 - 53: 8.466 distance: 48 - 87: 27.865 distance: 49 - 50: 41.363 distance: 49 - 51: 30.946 distance: 50 - 52: 16.370 distance: 53 - 54: 15.223 distance: 54 - 55: 25.498 distance: 54 - 57: 16.062 distance: 55 - 56: 40.118 distance: 55 - 64: 26.276 distance: 57 - 58: 20.439 distance: 58 - 59: 27.443 distance: 58 - 60: 41.911 distance: 59 - 61: 6.112 distance: 61 - 63: 40.008 distance: 62 - 63: 33.926 distance: 64 - 65: 18.676 distance: 65 - 66: 41.226 distance: 65 - 68: 35.631 distance: 66 - 67: 53.640 distance: 66 - 76: 47.437 distance: 68 - 69: 11.905 distance: 69 - 70: 21.267 distance: 69 - 71: 13.151 distance: 70 - 72: 16.210 distance: 71 - 73: 20.993 distance: 72 - 74: 11.933 distance: 73 - 74: 21.455 distance: 74 - 75: 14.492 distance: 76 - 77: 14.618 distance: 77 - 78: 27.629 distance: 77 - 80: 27.845 distance: 78 - 79: 12.383 distance: 78 - 87: 16.278 distance: 80 - 81: 12.970 distance: 81 - 82: 7.005 distance: 83 - 84: 5.853 distance: 84 - 85: 4.270 distance: 84 - 86: 5.938 distance: 87 - 88: 7.453 distance: 88 - 89: 21.555 distance: 88 - 91: 20.274 distance: 89 - 90: 15.920 distance: 91 - 92: 6.865