Starting phenix.real_space_refine on Thu Mar 21 18:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6j_24877/03_2024/7s6j_24877.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 144 5.16 5 C 19572 2.51 5 N 5106 2.21 5 O 5973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30795 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "B" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "E" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.97, per 1000 atoms: 0.52 Number of scatterers: 30795 At special positions: 0 Unit cell: (159.85, 170.2, 197.8, 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 144 16.00 O 5973 8.00 N 5106 7.00 C 19572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.20 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.10 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS E 383 " distance=2.20 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS E 985 " distance=2.20 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.07 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.10 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.05 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.07 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.09 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.01 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 234 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B 17 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 234 " " NAG E1301 " - " ASN E 709 " " NAG E1302 " - " ASN E1134 " " NAG E1303 " - " ASN E 17 " " NAG E1304 " - " ASN E 149 " " NAG E1305 " - " ASN E 234 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN E 717 " " NAG Q 1 " - " ASN E 801 " " NAG R 1 " - " ASN E1098 " Time building additional restraints: 11.83 Conformation dependent library (CDL) restraints added in 5.4 seconds 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 63 sheets defined 21.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.644A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.792A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.348A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.935A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.645A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.793A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.347A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.644A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.792A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.348A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 964 through 968 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR E 998 " --> pdb=" O ASP E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.597A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.351A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.506A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.184A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.484A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.848A pdb=" N THR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.598A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.352A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.505A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.183A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.483A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS E 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 703 " --> pdb=" O LYS E 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.598A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.598A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.766A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.848A pdb=" N THR C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 18 through 24 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.406A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS D 39 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.598A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS E 187 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 140 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE E 157 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.351A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL E 595 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 324 through 326 removed outlier: 6.183A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR E 696 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN E 658 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.847A pdb=" N THR F 33 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AG8, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS G 39 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) 1278 hydrogen bonds defined for protein. 3384 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: 16.09 Time building geometry restraints manager: 12.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6384 1.32 - 1.46: 10902 1.46 - 1.60: 13980 1.60 - 1.74: 57 1.74 - 1.88: 177 Bond restraints: 31500 Sorted by residual: bond pdb=" NE ARG B 634 " pdb=" CZ ARG B 634 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 5.02e+01 bond pdb=" NE ARG A 634 " pdb=" CZ ARG A 634 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG E 634 " pdb=" CZ ARG E 634 " ideal model delta sigma weight residual 1.326 1.403 -0.077 1.10e-02 8.26e+03 4.95e+01 bond pdb=" NE ARG C 95 " pdb=" CZ ARG C 95 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 3.01e+01 bond pdb=" NE ARG H 95 " pdb=" CZ ARG H 95 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 2.99e+01 ... (remaining 31495 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.33: 451 103.33 - 111.36: 12315 111.36 - 119.40: 13933 119.40 - 127.43: 15923 127.43 - 135.47: 236 Bond angle restraints: 42858 Sorted by residual: angle pdb=" N GLY F 106 " pdb=" CA GLY F 106 " pdb=" C GLY F 106 " ideal model delta sigma weight residual 111.70 123.12 -11.42 1.28e+00 6.10e-01 7.96e+01 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 111.70 123.09 -11.39 1.28e+00 6.10e-01 7.92e+01 angle pdb=" N GLY C 106 " pdb=" CA GLY C 106 " pdb=" C GLY C 106 " ideal model delta sigma weight residual 111.70 123.04 -11.34 1.28e+00 6.10e-01 7.85e+01 angle pdb=" C ASN E 81 " pdb=" N PRO E 82 " pdb=" CA PRO E 82 " ideal model delta sigma weight residual 120.31 128.69 -8.38 9.80e-01 1.04e+00 7.32e+01 angle pdb=" C ASN B 81 " pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 120.31 128.69 -8.38 9.80e-01 1.04e+00 7.31e+01 ... (remaining 42853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 18529 17.68 - 35.35: 491 35.35 - 53.03: 141 53.03 - 70.71: 75 70.71 - 88.38: 9 Dihedral angle restraints: 19245 sinusoidal: 7932 harmonic: 11313 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 160.00 -67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.98 -66.98 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS E 617 " pdb=" SG CYS E 617 " pdb=" SG CYS E 649 " pdb=" CB CYS E 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 19242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3457 0.102 - 0.204: 1173 0.204 - 0.306: 201 0.306 - 0.408: 71 0.408 - 0.510: 30 Chirality restraints: 4932 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 ... (remaining 4929 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.073 2.00e-02 2.50e+03 7.62e-02 7.25e+01 pdb=" CG ASN E 234 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.073 2.00e-02 2.50e+03 7.61e-02 7.23e+01 pdb=" CG ASN A 234 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.117 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.073 2.00e-02 2.50e+03 7.60e-02 7.23e+01 pdb=" CG ASN B 234 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.093 2.00e-02 2.50e+03 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 12580 2.90 - 3.40: 28437 3.40 - 3.90: 53403 3.90 - 4.40: 61951 4.40 - 4.90: 99959 Nonbonded interactions: 256330 Sorted by model distance: nonbonded pdb=" N ASN B 185 " pdb=" O ASN B 185 " model vdw 2.401 2.496 nonbonded pdb=" N ASN A 185 " pdb=" O ASN A 185 " model vdw 2.402 2.496 nonbonded pdb=" N ASN E 185 " pdb=" O ASN E 185 " model vdw 2.402 2.496 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.413 2.520 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.414 2.520 ... (remaining 256325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 13.460 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 85.140 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.020 0.145 31500 Z= 1.309 Angle : 1.803 11.433 42858 Z= 1.213 Chirality : 0.110 0.510 4932 Planarity : 0.009 0.050 5502 Dihedral : 9.983 88.383 11832 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 3852 helix: 0.23 (0.18), residues: 648 sheet: 0.76 (0.17), residues: 945 loop : -0.15 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.011 TRP E 64 HIS 0.012 0.003 HIS C 100G PHE 0.050 0.006 PHE E 55 TYR 0.093 0.009 TYR E 37 ARG 0.013 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 581 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.3965 (m-80) cc_final: 0.3178 (m-80) REVERT: A 177 MET cc_start: 0.7446 (mtp) cc_final: 0.6772 (mtm) REVERT: A 205 SER cc_start: 0.8229 (p) cc_final: 0.7544 (p) REVERT: A 269 TYR cc_start: 0.7191 (m-80) cc_final: 0.6718 (m-80) REVERT: A 338 PHE cc_start: 0.7487 (m-80) cc_final: 0.7266 (m-80) REVERT: A 342 PHE cc_start: 0.7601 (m-80) cc_final: 0.7275 (m-80) REVERT: A 428 ASP cc_start: 0.8499 (t0) cc_final: 0.8177 (p0) REVERT: A 456 PHE cc_start: 0.6884 (m-80) cc_final: 0.4995 (m-80) REVERT: H 54 LEU cc_start: 0.7411 (mt) cc_final: 0.6817 (mt) REVERT: H 68 THR cc_start: 0.5519 (p) cc_final: 0.4556 (p) REVERT: H 80 MET cc_start: 0.1473 (ttp) cc_final: 0.0482 (ppp) REVERT: L 4 MET cc_start: 0.4435 (mmm) cc_final: 0.3858 (mmm) REVERT: B 160 TYR cc_start: 0.4066 (m-80) cc_final: 0.3258 (m-80) REVERT: B 177 MET cc_start: 0.7386 (mtp) cc_final: 0.6631 (mtm) REVERT: B 201 PHE cc_start: 0.7807 (t80) cc_final: 0.7478 (t80) REVERT: B 402 ILE cc_start: 0.8030 (pt) cc_final: 0.7651 (pt) REVERT: B 428 ASP cc_start: 0.8272 (t0) cc_final: 0.7954 (p0) REVERT: B 456 PHE cc_start: 0.7045 (m-80) cc_final: 0.4990 (m-80) REVERT: C 48 MET cc_start: 0.6766 (mtm) cc_final: 0.6515 (mtt) REVERT: C 54 LEU cc_start: 0.7391 (mt) cc_final: 0.6754 (mp) REVERT: C 68 THR cc_start: 0.5648 (p) cc_final: 0.4956 (p) REVERT: C 80 MET cc_start: 0.0702 (ttp) cc_final: 0.0417 (ppp) REVERT: D 4 MET cc_start: 0.4422 (mmm) cc_final: 0.3864 (mmm) REVERT: E 61 ASN cc_start: 0.7034 (m-40) cc_final: 0.6492 (p0) REVERT: E 160 TYR cc_start: 0.3888 (m-80) cc_final: 0.2944 (m-80) REVERT: E 177 MET cc_start: 0.7347 (mtp) cc_final: 0.6955 (mtm) REVERT: E 326 ILE cc_start: 0.7959 (mt) cc_final: 0.7650 (mm) REVERT: E 456 PHE cc_start: 0.7021 (m-80) cc_final: 0.5130 (m-80) REVERT: E 461 LEU cc_start: 0.8731 (mt) cc_final: 0.8459 (mt) REVERT: F 54 LEU cc_start: 0.7640 (mt) cc_final: 0.7168 (mp) REVERT: F 68 THR cc_start: 0.5281 (p) cc_final: 0.4751 (p) REVERT: F 80 MET cc_start: 0.1100 (ttp) cc_final: 0.0192 (ppp) REVERT: G 4 MET cc_start: 0.4270 (mmm) cc_final: 0.3787 (mmm) outliers start: 6 outliers final: 3 residues processed: 587 average time/residue: 0.4658 time to fit residues: 418.4427 Evaluate side-chains 233 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 230 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 351 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 317 ASN A 360 ASN A 804 GLN A 907 ASN A 913 GLN A1119 ASN H 39 GLN L 38 GLN B 49 HIS B 360 ASN B 907 ASN B 913 GLN B1119 ASN C 39 GLN D 38 GLN E 49 HIS E 317 ASN E 360 ASN E 613 GLN E 907 ASN E 913 GLN E1119 ASN F 39 GLN F 61 GLN G 37 GLN G 38 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31500 Z= 0.244 Angle : 0.727 7.930 42858 Z= 0.389 Chirality : 0.049 0.229 4932 Planarity : 0.005 0.047 5502 Dihedral : 6.765 59.600 4896 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.24 % Allowed : 5.82 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3852 helix: 1.82 (0.20), residues: 642 sheet: 0.34 (0.16), residues: 981 loop : -0.60 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 64 HIS 0.004 0.001 HIS E1064 PHE 0.030 0.002 PHE C 100H TYR 0.028 0.002 TYR F 91 ARG 0.005 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 287 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.3885 (m-80) cc_final: 0.3022 (m-80) REVERT: A 269 TYR cc_start: 0.7181 (m-80) cc_final: 0.6618 (m-80) REVERT: A 338 PHE cc_start: 0.7480 (m-80) cc_final: 0.7242 (m-80) REVERT: A 342 PHE cc_start: 0.7677 (m-80) cc_final: 0.7285 (m-80) REVERT: A 428 ASP cc_start: 0.8655 (t0) cc_final: 0.8273 (p0) REVERT: A 456 PHE cc_start: 0.6891 (m-80) cc_final: 0.6630 (m-80) REVERT: A 988 GLU cc_start: 0.7472 (mp0) cc_final: 0.7252 (pm20) REVERT: H 80 MET cc_start: 0.1422 (ttp) cc_final: 0.0497 (ppp) REVERT: H 90 TYR cc_start: 0.5665 (p90) cc_final: 0.5361 (p90) REVERT: L 4 MET cc_start: 0.4314 (mmm) cc_final: 0.3070 (mpp) REVERT: B 160 TYR cc_start: 0.3781 (m-80) cc_final: 0.2711 (m-80) REVERT: B 177 MET cc_start: 0.7144 (mtp) cc_final: 0.6738 (mtm) REVERT: B 192 PHE cc_start: 0.7818 (m-10) cc_final: 0.7422 (m-10) REVERT: B 205 SER cc_start: 0.8118 (p) cc_final: 0.7212 (t) REVERT: B 212 LEU cc_start: 0.7360 (tp) cc_final: 0.6843 (mt) REVERT: B 456 PHE cc_start: 0.6886 (m-80) cc_final: 0.6588 (m-80) REVERT: B 529 LYS cc_start: 0.7901 (pptt) cc_final: 0.7647 (pptt) REVERT: C 80 MET cc_start: 0.0732 (ttp) cc_final: 0.0005 (ppp) REVERT: D 4 MET cc_start: 0.4507 (mmm) cc_final: 0.3924 (mmm) REVERT: D 32 TYR cc_start: 0.5865 (m-80) cc_final: 0.5607 (m-80) REVERT: D 50 ASP cc_start: 0.7464 (t0) cc_final: 0.7250 (t70) REVERT: D 91 PRO cc_start: 0.6108 (Cg_exo) cc_final: 0.5858 (Cg_endo) REVERT: E 61 ASN cc_start: 0.6808 (m-40) cc_final: 0.6444 (p0) REVERT: E 160 TYR cc_start: 0.3757 (m-80) cc_final: 0.3004 (m-80) REVERT: E 192 PHE cc_start: 0.7532 (m-80) cc_final: 0.7155 (m-80) REVERT: E 205 SER cc_start: 0.7825 (p) cc_final: 0.7053 (t) REVERT: E 456 PHE cc_start: 0.6734 (m-80) cc_final: 0.6453 (m-80) REVERT: E 461 LEU cc_start: 0.8642 (mt) cc_final: 0.8353 (mt) REVERT: E 517 LEU cc_start: 0.6992 (mt) cc_final: 0.6221 (mp) REVERT: F 80 MET cc_start: 0.1316 (ttp) cc_final: 0.0270 (ppp) REVERT: F 90 TYR cc_start: 0.5900 (p90) cc_final: 0.5426 (p90) REVERT: G 4 MET cc_start: 0.4471 (mmm) cc_final: 0.4040 (mmm) REVERT: G 50 ASP cc_start: 0.7807 (t0) cc_final: 0.7476 (t70) outliers start: 42 outliers final: 22 residues processed: 320 average time/residue: 0.3970 time to fit residues: 207.2615 Evaluate side-chains 237 residues out of total 3387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9213 > 50: distance: 8 - 11: 26.050 distance: 11 - 12: 43.155 distance: 12 - 13: 38.810 distance: 12 - 15: 29.524 distance: 13 - 14: 17.025 distance: 13 - 18: 48.126 distance: 15 - 16: 30.661 distance: 15 - 17: 27.596 distance: 18 - 19: 22.254 distance: 18 - 142: 30.457 distance: 19 - 20: 22.009 distance: 19 - 22: 28.007 distance: 20 - 21: 31.057 distance: 20 - 26: 23.935 distance: 21 - 153: 24.076 distance: 22 - 23: 13.321 distance: 23 - 25: 7.356 distance: 26 - 27: 12.567 distance: 27 - 28: 41.687 distance: 27 - 30: 5.363 distance: 28 - 29: 42.356 distance: 28 - 32: 55.252 distance: 30 - 31: 12.635 distance: 32 - 33: 50.724 distance: 32 - 156: 36.933 distance: 33 - 34: 43.885 distance: 33 - 36: 40.100 distance: 34 - 35: 42.232 distance: 34 - 40: 18.244 distance: 36 - 37: 35.909 distance: 37 - 39: 23.055 distance: 40 - 41: 20.994 distance: 41 - 42: 37.010 distance: 41 - 44: 54.777 distance: 42 - 43: 59.649 distance: 42 - 46: 29.559 distance: 44 - 45: 44.800 distance: 46 - 47: 20.353 distance: 46 - 52: 33.141 distance: 47 - 48: 12.847 distance: 47 - 50: 31.827 distance: 48 - 49: 26.215 distance: 48 - 53: 22.310 distance: 50 - 51: 13.013 distance: 51 - 52: 27.596 distance: 53 - 54: 23.325 distance: 54 - 55: 28.613 distance: 55 - 56: 19.946 distance: 55 - 57: 42.069 distance: 57 - 58: 16.539 distance: 58 - 59: 28.043 distance: 58 - 61: 30.202 distance: 59 - 60: 28.249 distance: 59 - 66: 20.889 distance: 61 - 62: 34.180 distance: 62 - 63: 18.331 distance: 63 - 64: 20.344 distance: 63 - 65: 10.288 distance: 66 - 67: 22.784 distance: 67 - 68: 40.568 distance: 67 - 70: 57.551 distance: 68 - 69: 34.409 distance: 68 - 77: 46.332 distance: 71 - 72: 23.869 distance: 72 - 73: 21.512 distance: 73 - 74: 9.244 distance: 74 - 75: 10.839 distance: 74 - 76: 11.133 distance: 77 - 78: 31.775 distance: 77 - 104: 18.103 distance: 78 - 79: 35.759 distance: 78 - 81: 26.355 distance: 79 - 80: 40.267 distance: 79 - 82: 24.970 distance: 80 - 101: 25.793