Starting phenix.real_space_refine on Tue Aug 26 04:03:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9j_8785/08_2025/5w9j_8785.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9j_8785/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/5w9j_8785/08_2025/5w9j_8785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9j_8785/08_2025/5w9j_8785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9j_8785/08_2025/5w9j_8785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9j_8785/08_2025/5w9j_8785.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.26, per 1000 atoms: 0.22 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.77 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: 9.50 Time building geometry restraints manager: 3.90 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: 0.09 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'C' 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 'D' selection = chain 'A' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'C' 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- 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 : 5.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG D 979 TYR 0.046 0.006 TYR L 438 PHE 0.035 0.004 PHE F 71 TRP 0.039 0.007 TRP G1184 HIS 0.009 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.01349 (33735) covalent geometry : angle 1.56938 (45876) SS BOND : bond 0.20103 ( 57) SS BOND : angle 3.57043 ( 114) hydrogen bonds : bond 0.15960 ( 1244) hydrogen bonds : angle 8.99853 ( 3534) *********************** 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 : 0.138 Fit side-chains revert: symmetry clash REVERT: D 796 GLN cc_start: 0.9076 (tt0) cc_final: 0.8649 (tm-30) REVERT: D 906 MET cc_start: 0.2203 (ttt) cc_final: 0.1996 (mmt) REVERT: D 909 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.3673 (p90) REVERT: D 1012 PHE cc_start: 0.8741 (m-80) cc_final: 0.8509 (m-10) REVERT: D 1134 LEU cc_start: 0.9306 (mt) cc_final: 0.8750 (pt) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.0787 time to fit residues: 5.9538 Evaluate side-chains 24 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.151 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 : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0916 time to fit residues: 2.1688 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 : 0.038 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 : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLU cc_start: 0.7827 (tp30) cc_final: 0.7278 (mp0) REVERT: F 70 ASP cc_start: 0.8380 (t0) cc_final: 0.7727 (m-30) REVERT: F 90 GLN cc_start: 0.8292 (tp40) cc_final: 0.7825 (pp30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0652 time to fit residues: 2.3285 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 : 0.034 Evaluate side-chains 81 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.233 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: 0.0757 time to fit residues: 8.1651 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.0050 chunk 388 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 0.1980 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 0.7980 overall best weight: 0.0636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050329 restraints weight = 24315.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051571 restraints weight = 15374.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052435 restraints weight = 10846.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053031 restraints weight = 8297.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053412 restraints weight = 6755.623| |-----------------------------------------------------------------------------| r_work (final): 0.3110 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.045780 restraints weight = 9283.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046877 restraints weight = 6169.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047677 restraints weight = 4433.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048275 restraints weight = 3337.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048718 restraints weight = 2617.845| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050671 restraints weight = 7953.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051775 restraints weight = 5648.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052572 restraints weight = 4265.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053118 restraints weight = 3419.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053499 restraints weight = 2856.424| |-----------------------------------------------------------------------------| r_work (final): 0.3396 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.057022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.046659 restraints weight = 63915.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.047689 restraints weight = 42301.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.048417 restraints weight = 30986.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.048859 restraints weight = 24500.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.049201 restraints weight = 20518.680| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33792 Z= 0.158 Angle : 0.717 8.554 45990 Z= 0.394 Chirality : 0.045 0.186 5091 Planarity : 0.008 0.094 5961 Dihedral : 5.930 36.896 4629 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.26 % Favored : 95.24 % Rotamer: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 4227 helix: 0.90 (0.19), residues: 696 sheet: 0.14 (0.15), residues: 1023 loop : 0.10 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 181 TYR 0.020 0.002 TYR D1141 PHE 0.023 0.002 PHE C 87 TRP 0.030 0.002 TRP B 47 HIS 0.006 0.001 HIS K 681 Details of bonding type rmsd covalent geometry : bond 0.00329 (33735) covalent geometry : angle 0.70922 (45876) SS BOND : bond 0.00568 ( 57) SS BOND : angle 2.17055 ( 114) hydrogen bonds : bond 0.05452 ( 1244) hydrogen bonds : angle 6.89659 ( 3534) *********************** 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 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 796 GLN cc_start: 0.9037 (tt0) cc_final: 0.8726 (tm-30) REVERT: D 925 CYS cc_start: 0.1274 (OUTLIER) cc_final: 0.0968 (p) REVERT: D 928 TYR cc_start: 0.6203 (p90) cc_final: 0.5920 (t80) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0471 time to fit residues: 3.1417 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 : 0.131 Evaluate side-chains 21 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8550 (m-40) cc_final: 0.8339 (m110) REVERT: E 69 MET cc_start: 0.6772 (tpt) cc_final: 0.6534 (mmm) REVERT: E 105 GLN cc_start: 0.8220 (pm20) cc_final: 0.7905 (pm20) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0920 time to fit residues: 2.0732 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.038 Evaluate side-chains 25 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 70 ASP cc_start: 0.8110 (t0) cc_final: 0.7393 (m-30) REVERT: F 90 GLN cc_start: 0.7631 (tp40) cc_final: 0.7008 (pp30) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0698 time to fit residues: 1.8861 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: K 116 PHE cc_start: 0.7823 (p90) cc_final: 0.7408 (p90) REVERT: K 288 ASP cc_start: 0.7436 (m-30) cc_final: 0.6978 (t0) REVERT: K 452 MET cc_start: 0.4142 (ttm) cc_final: 0.3732 (ptm) REVERT: K 511 ARG cc_start: 0.3053 (mtm-85) cc_final: 0.2559 (ttt180) REVERT: K 611 VAL cc_start: 0.9135 (p) cc_final: 0.8931 (m) REVERT: K 638 LEU cc_start: 0.8842 (tp) cc_final: 0.8602 (tp) REVERT: K 696 MET cc_start: 0.5581 (pmm) cc_final: 0.5327 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0669 time to fit residues: 5.4195 Evaluate side-chains 39 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 272 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 251 optimal weight: 0.2980 chunk 405 optimal weight: 0.0570 chunk 211 optimal weight: 7.9990 chunk 392 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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** D 914 GLN D1097 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... Flipped N/Q/H residues before XYZ refinement: I 38 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 K 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049684 restraints weight = 23745.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050917 restraints weight = 15026.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051827 restraints weight = 10625.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052479 restraints weight = 8157.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053029 restraints weight = 6669.900| |-----------------------------------------------------------------------------| r_work (final): 0.3100 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.044606 restraints weight = 10471.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.045833 restraints weight = 6568.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.046664 restraints weight = 4483.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047257 restraints weight = 3317.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047754 restraints weight = 2578.107| |-----------------------------------------------------------------------------| r_work (final): 0.3237 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.060378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.053532 restraints weight = 8126.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.054495 restraints weight = 6017.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.055250 restraints weight = 4672.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.055822 restraints weight = 3801.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056180 restraints weight = 3192.913| |-----------------------------------------------------------------------------| r_work (final): 0.3429 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.056548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.046460 restraints weight = 68374.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.047454 restraints weight = 44457.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.048148 restraints weight = 31992.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.048588 restraints weight = 25058.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048910 restraints weight = 20886.697| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 33792 Z= 0.208 Angle : 0.943 23.085 45990 Z= 0.493 Chirality : 0.081 2.003 5091 Planarity : 0.009 0.129 5961 Dihedral : 6.079 33.730 4629 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.40 % Favored : 95.10 % Rotamer: Outliers : 0.99 % Allowed : 2.87 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.13), residues: 4227 helix: 0.17 (0.19), residues: 687 sheet: -0.21 (0.15), residues: 984 loop : -0.12 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG G 822 TYR 0.124 0.004 TYR A1141 PHE 0.135 0.005 PHE A 895 TRP 0.063 0.005 TRP F 35 HIS 0.104 0.006 HIS G 836 Details of bonding type rmsd covalent geometry : bond 0.00460 (33735) covalent geometry : angle 0.93460 (45876) SS BOND : bond 0.00741 ( 57) SS BOND : angle 2.63850 ( 114) hydrogen bonds : bond 0.05864 ( 1244) hydrogen bonds : angle 7.03720 ( 3534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 925 CYS cc_start: 0.1739 (OUTLIER) cc_final: 0.1155 (p) REVERT: D 928 TYR cc_start: 0.6348 (p90) cc_final: 0.6055 (t80) outliers start: 9 outliers final: 1 residues processed: 38 average time/residue: 0.0414 time to fit residues: 2.3287 Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.142 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ASN cc_start: 0.8344 (m-40) cc_final: 0.8112 (m110) REVERT: E 57 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7256 (t) outliers start: 3 outliers final: 1 residues processed: 17 average time/residue: 0.0772 time to fit residues: 1.4387 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.042 Evaluate side-chains 21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 ASP cc_start: 0.8333 (t0) cc_final: 0.7711 (m-30) REVERT: I 73 LEU cc_start: 0.8264 (tp) cc_final: 0.8063 (tp) REVERT: I 85 MET cc_start: 0.7230 (tpt) cc_final: 0.6431 (tpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0524 time to fit residues: 1.2283 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.037 Evaluate side-chains 46 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8106 (m-80) cc_final: 0.7891 (m-80) REVERT: K 288 ASP cc_start: 0.7358 (m-30) cc_final: 0.6867 (t0) REVERT: K 452 MET cc_start: 0.4322 (ttm) cc_final: 0.4005 (ptm) REVERT: K 511 ARG cc_start: 0.2996 (mtm-85) cc_final: 0.2484 (ttt180) REVERT: K 638 LEU cc_start: 0.8795 (tp) cc_final: 0.8576 (tp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0722 time to fit residues: 4.6973 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 294 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 414 optimal weight: 0.0970 chunk 272 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 289 optimal weight: 0.0370 chunk 217 optimal weight: 0.2980 chunk 248 optimal weight: 40.0000 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 836 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 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: ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046921 restraints weight = 27372.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048203 restraints weight = 16917.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049047 restraints weight = 11781.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049744 restraints weight = 8951.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050116 restraints weight = 7123.121| |-----------------------------------------------------------------------------| r_work (final): 0.3067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.050826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044297 restraints weight = 12273.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045366 restraints weight = 8251.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046166 restraints weight = 6072.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046781 restraints weight = 4717.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047230 restraints weight = 3811.196| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.052885 restraints weight = 7896.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.053840 restraints weight = 5483.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054567 restraints weight = 4243.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.055009 restraints weight = 3475.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055421 restraints weight = 3029.153| |-----------------------------------------------------------------------------| r_work (final): 0.3429 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.056409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.046388 restraints weight = 67674.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047319 restraints weight = 44721.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.047997 restraints weight = 32510.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.048466 restraints weight = 25593.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.048771 restraints weight = 21343.567| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.001 33792 Z= 0.613 Angle : 1.016 40.908 45990 Z= 0.525 Chirality : 0.081 2.003 5091 Planarity : 0.009 0.129 5961 Dihedral : 6.079 33.730 4629 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.40 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.13), residues: 4227 helix: 0.17 (0.19), residues: 687 sheet: -0.21 (0.15), residues: 984 loop : -0.12 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG D 822 TYR 0.124 0.004 TYR A1141 PHE 0.135 0.005 PHE A 895 TRP 0.063 0.005 TRP I 35 HIS 0.104 0.006 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00461 (33735) covalent geometry : angle 0.93461 (45876) SS BOND : bond 0.28096 ( 57) SS BOND : angle 8.05406 ( 114) hydrogen bonds : bond 0.05864 ( 1244) hydrogen bonds : angle 7.03720 ( 3534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 927 GLN cc_start: 0.7093 (mt0) cc_final: 0.6122 (pp30) REVERT: G 928 TYR cc_start: 0.6083 (p90) cc_final: 0.5759 (t80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0526 time to fit residues: 2.1476 Evaluate side-chains 21 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.106 Evaluate side-chains 14 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0970 time to fit residues: 1.4841 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.040 Evaluate side-chains 20 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.6594 (mp) cc_final: 0.6124 (mt) REVERT: F 33 MET cc_start: 0.5809 (mmp) cc_final: 0.5329 (mmp) REVERT: F 70 ASP cc_start: 0.7699 (t0) cc_final: 0.7200 (m-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0606 time to fit residues: 1.3360 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.034 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 PHE cc_start: 0.8219 (m-80) cc_final: 0.7928 (m-80) REVERT: K 288 ASP cc_start: 0.7420 (m-30) cc_final: 0.6886 (t0) REVERT: K 452 MET cc_start: 0.4329 (ttm) cc_final: 0.4019 (ptm) REVERT: K 511 ARG cc_start: 0.2987 (mtm-85) cc_final: 0.2495 (ttt180) REVERT: K 638 LEU cc_start: 0.8781 (tp) cc_final: 0.8569 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0654 time to fit residues: 4.0082 Evaluate side-chains 36 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2644 > 50: distance: 1 - 2: 5.417 distance: 2 - 3: 4.739 distance: 2 - 5: 7.114 distance: 3 - 4: 13.092 distance: 3 - 7: 16.231 distance: 5 - 6: 11.562 distance: 7 - 8: 10.344 distance: 8 - 9: 7.856 distance: 8 - 11: 14.831 distance: 9 - 10: 19.386 distance: 9 - 12: 24.208 distance: 12 - 13: 15.905 distance: 13 - 14: 17.603 distance: 13 - 16: 12.591 distance: 14 - 15: 8.469 distance: 14 - 18: 13.097 distance: 15 - 38: 18.694 distance: 16 - 17: 11.604 distance: 18 - 19: 5.562 distance: 19 - 20: 3.285 distance: 19 - 22: 6.731 distance: 20 - 21: 7.583 distance: 20 - 26: 11.469 distance: 21 - 46: 29.911 distance: 22 - 23: 14.183 distance: 22 - 24: 12.286 distance: 23 - 25: 3.992 distance: 26 - 27: 18.714 distance: 27 - 28: 12.730 distance: 28 - 29: 20.298 distance: 28 - 30: 8.603 distance: 29 - 54: 18.392 distance: 30 - 31: 13.398 distance: 31 - 32: 11.938 distance: 31 - 34: 13.285 distance: 32 - 33: 12.400 distance: 32 - 38: 11.117 distance: 33 - 63: 29.254 distance: 35 - 36: 9.264 distance: 35 - 37: 13.896 distance: 38 - 39: 15.275 distance: 39 - 40: 9.726 distance: 39 - 42: 14.674 distance: 40 - 41: 15.967 distance: 40 - 46: 10.557 distance: 42 - 43: 29.485 distance: 42 - 44: 33.496 distance: 43 - 45: 18.692 distance: 46 - 47: 6.451 distance: 47 - 48: 14.412 distance: 47 - 50: 22.059 distance: 48 - 54: 32.644 distance: 50 - 51: 19.950 distance: 50 - 52: 7.936 distance: 51 - 53: 27.729 distance: 54 - 55: 15.885 distance: 55 - 56: 20.757 distance: 55 - 58: 17.782 distance: 56 - 57: 13.678 distance: 56 - 63: 12.203 distance: 58 - 59: 35.917 distance: 59 - 60: 22.623 distance: 60 - 61: 11.260 distance: 60 - 62: 16.600 distance: 63 - 64: 5.333 distance: 64 - 65: 24.230 distance: 64 - 67: 6.391 distance: 65 - 66: 14.839 distance: 65 - 74: 28.764 distance: 67 - 68: 29.460 distance: 68 - 69: 16.944 distance: 69 - 70: 8.258 distance: 70 - 71: 17.343 distance: 71 - 72: 9.022 distance: 71 - 73: 7.885 distance: 74 - 75: 25.135 distance: 75 - 76: 8.254 distance: 75 - 78: 20.453 distance: 76 - 77: 9.291