Starting phenix.real_space_refine on Thu Mar 21 18:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/03_2024/7s6k_24878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/03_2024/7s6k_24878.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/7s6k_24878/03_2024/7s6k_24878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/03_2024/7s6k_24878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/03_2024/7s6k_24878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6k_24878/03_2024/7s6k_24878.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= -0.000 sd= 0.036 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 19641 2.51 5 N 5100 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30903 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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: "S" 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: "T" 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: "U" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.72, per 1000 atoms: 0.51 Number of scatterers: 30903 At special positions: 0 Unit cell: (151.8, 157.55, 205.85, 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 6018 8.00 N 5100 7.00 C 19641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 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 E 985 " distance=2.32 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS B 383 " distance=2.32 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 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 985 " - pdb=" SG CYS E 383 " distance=2.32 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 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG E1301 " - " ASN E 616 " " NAG E1302 " - " ASN E 709 " " NAG E1303 " - " ASN E 343 " " NAG E1304 " - " ASN E 61 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E1074 " " NAG E1307 " - " ASN E 17 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 11.99 Conformation dependent library (CDL) restraints added in 5.2 seconds 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7242 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 20.5% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 27 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 52A through 55 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.815A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.816A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.837A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE B 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.505A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.394A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN E 188 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 210 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG E 190 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR E 208 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE E 192 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS E 206 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE E 194 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR E 204 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN E 196 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS E 202 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.398A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.880A 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: 6.815A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE E 238 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN E 137 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR E 240 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU E 242 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 324 through 326 removed outlier: 6.376A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.938A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU E 516 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 395 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER E 514 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E 397 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 512 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER E 399 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 510 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL E 401 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR E 508 " --> pdb=" O VAL E 401 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.028A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 33 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 1256 hydrogen bonds defined for protein. 3354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.43 Time building geometry restraints manager: 12.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5305 1.31 - 1.45: 10202 1.45 - 1.59: 15840 1.59 - 1.73: 87 1.73 - 1.87: 177 Bond restraints: 31611 Sorted by residual: bond pdb=" CB PHE F 100H" pdb=" CG PHE F 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.28e+01 bond pdb=" CB PHE H 100H" pdb=" CG PHE H 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.24e+01 bond pdb=" CB PHE C 100H" pdb=" CG PHE C 100H" ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.19e+01 bond pdb=" CZ2 TRP A 152 " pdb=" CH2 TRP A 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.12e+01 bond pdb=" CZ2 TRP B 152 " pdb=" CH2 TRP B 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.10e+01 ... (remaining 31606 not shown) Histogram of bond angle deviations from ideal: 95.03 - 108.04: 2565 108.04 - 121.05: 31356 121.05 - 134.06: 9081 134.06 - 147.07: 9 147.07 - 160.08: 3 Bond angle restraints: 43014 Sorted by residual: angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.08 -35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG R 1 " pdb=" N2 NAG R 1 " pdb=" C7 NAG R 1 " ideal model delta sigma weight residual 124.56 160.06 -35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 124.56 160.04 -35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N GLY A 261 " pdb=" CA GLY A 261 " pdb=" C GLY A 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.09e+01 angle pdb=" N GLY E 261 " pdb=" CA GLY E 261 " pdb=" C GLY E 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.08e+01 ... (remaining 43009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 18757 17.50 - 34.99: 476 34.99 - 52.49: 96 52.49 - 69.98: 84 69.98 - 87.48: 15 Dihedral angle restraints: 19428 sinusoidal: 8145 harmonic: 11283 Sorted by residual: dihedral pdb=" CB CYS B 985 " pdb=" SG CYS B 985 " pdb=" SG CYS E 383 " pdb=" CB CYS E 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS E 985 " pdb=" CB CYS E 985 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 985 " pdb=" SG CYS A 985 " pdb=" SG CYS B 383 " pdb=" CB CYS B 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 19425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3466 0.098 - 0.197: 1144 0.197 - 0.295: 226 0.295 - 0.394: 87 0.394 - 0.492: 60 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+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 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 4980 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.075 2.00e-02 2.50e+03 8.14e-02 8.28e+01 pdb=" CG ASN A1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" CG ASN E1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.25e+01 pdb=" CG ASN B1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.096 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 12195 2.89 - 3.40: 28473 3.40 - 3.90: 53262 3.90 - 4.40: 61444 4.40 - 4.90: 99552 Nonbonded interactions: 254926 Sorted by model distance: nonbonded pdb=" N TYR B 351 " pdb=" N ALA B 352 " model vdw 2.392 2.560 nonbonded pdb=" N TYR E 351 " pdb=" N ALA E 352 " model vdw 2.393 2.560 nonbonded pdb=" N TYR A 351 " pdb=" N ALA A 352 " model vdw 2.393 2.560 nonbonded pdb=" NZ LYS B 854 " pdb=" OD2 ASP E 614 " model vdw 2.395 2.520 nonbonded pdb=" NZ LYS A 854 " pdb=" OD2 ASP B 614 " model vdw 2.395 2.520 ... (remaining 254921 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.560 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 84.970 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.158 31611 Z= 1.320 Angle : 1.793 35.518 43014 Z= 1.194 Chirality : 0.114 0.492 4983 Planarity : 0.008 0.036 5499 Dihedral : 9.772 87.478 12042 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.43 (0.13), residues: 3837 helix: 0.44 (0.19), residues: 648 sheet: 1.25 (0.16), residues: 933 loop : -0.12 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.011 TRP C 36 HIS 0.008 0.003 HIS B1048 PHE 0.035 0.006 PHE B 329 TYR 0.047 0.008 TYR B 38 ARG 0.009 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 717 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8403 (p90) cc_final: 0.8092 (p90) REVERT: A 395 VAL cc_start: 0.8817 (t) cc_final: 0.8586 (t) REVERT: A 1031 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8275 (mt-10) REVERT: H 32 TYR cc_start: 0.7387 (m-80) cc_final: 0.6856 (m-80) REVERT: L 32 TYR cc_start: 0.5904 (m-80) cc_final: 0.5558 (m-10) REVERT: L 48 ILE cc_start: 0.6292 (mt) cc_final: 0.6036 (mt) REVERT: B 140 PHE cc_start: 0.8332 (p90) cc_final: 0.8090 (p90) REVERT: B 473 TYR cc_start: 0.6994 (t80) cc_final: 0.6740 (t80) REVERT: B 764 ASN cc_start: 0.7825 (t0) cc_final: 0.7540 (t0) REVERT: B 1031 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8132 (mt-10) REVERT: C 32 TYR cc_start: 0.7427 (m-80) cc_final: 0.7209 (m-80) REVERT: F 32 TYR cc_start: 0.7332 (m-80) cc_final: 0.6886 (m-80) REVERT: F 33 THR cc_start: 0.8209 (m) cc_final: 0.7999 (p) REVERT: F 63 PHE cc_start: 0.7908 (m-80) cc_final: 0.7703 (m-10) REVERT: F 109 VAL cc_start: 0.7206 (t) cc_final: 0.6713 (t) REVERT: G 48 ILE cc_start: 0.6418 (mt) cc_final: 0.6141 (mt) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.4796 time to fit residues: 522.6987 Evaluate side-chains 369 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 303 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 351 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 188 ASN A 532 ASN A 762 GLN A 784 GLN A 914 ASN A 955 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 532 ASN B 762 GLN B 784 GLN B 914 ASN B 955 ASN B 992 GLN B1119 ASN E 30 ASN E 762 GLN E 784 GLN E 914 ASN E 992 GLN E1119 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31611 Z= 0.281 Angle : 0.714 10.315 43014 Z= 0.380 Chirality : 0.049 0.375 4983 Planarity : 0.005 0.058 5499 Dihedral : 5.842 32.714 5130 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.92 % Allowed : 6.69 % Favored : 91.39 % 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: 0.32 (0.13), residues: 3837 helix: 1.65 (0.19), residues: 657 sheet: 0.63 (0.16), residues: 972 loop : -0.40 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 35 HIS 0.012 0.001 HIS B 245 PHE 0.022 0.002 PHE E 347 TYR 0.029 0.002 TYR E 351 ARG 0.010 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 450 time to evaluate : 3.812 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 376 THR cc_start: 0.8796 (m) cc_final: 0.8347 (p) REVERT: A 984 LEU cc_start: 0.8236 (tp) cc_final: 0.7990 (tp) REVERT: A 994 ASP cc_start: 0.7703 (t0) cc_final: 0.7433 (t0) REVERT: A 1002 GLN cc_start: 0.8148 (tp40) cc_final: 0.7940 (tp40) REVERT: H 36 TRP cc_start: 0.7478 (m100) cc_final: 0.7255 (m100) REVERT: B 140 PHE cc_start: 0.8754 (p90) cc_final: 0.8284 (p90) REVERT: B 376 THR cc_start: 0.8803 (m) cc_final: 0.8405 (p) REVERT: B 574 ASP cc_start: 0.7700 (t0) cc_final: 0.7455 (t0) REVERT: B 992 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6907 (mm-40) REVERT: C 36 TRP cc_start: 0.7242 (m100) cc_final: 0.6066 (m100) REVERT: C 61 GLN cc_start: 0.7626 (tp40) cc_final: 0.7001 (pp30) REVERT: E 376 THR cc_start: 0.8787 (m) cc_final: 0.8341 (p) REVERT: E 992 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6724 (mm-40) REVERT: F 61 GLN cc_start: 0.7707 (tp40) cc_final: 0.7161 (pp30) REVERT: G 14 SER cc_start: 0.7522 (m) cc_final: 0.7174 (p) REVERT: G 32 TYR cc_start: 0.6038 (m-80) cc_final: 0.5738 (m-10) outliers start: 65 outliers final: 38 residues processed: 484 average time/residue: 0.4416 time to fit residues: 334.9224 Evaluate side-chains 393 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 353 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 380 optimal weight: 50.0000 chunk 313 optimal weight: 4.9990 chunk 349 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 762 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 245 HIS B 655 HIS B 755 GLN B 762 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 564 GLN E 655 HIS E 755 GLN E 762 GLN E 955 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100GHIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 31611 Z= 0.410 Angle : 0.694 10.135 43014 Z= 0.366 Chirality : 0.049 0.312 4983 Planarity : 0.005 0.073 5499 Dihedral : 5.718 36.051 5130 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 2.52 % Allowed : 8.44 % Favored : 89.05 % 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: -0.02 (0.13), residues: 3837 helix: 1.73 (0.20), residues: 642 sheet: 0.20 (0.15), residues: 1071 loop : -0.65 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.006 0.002 HIS B 655 PHE 0.023 0.002 PHE A 497 TYR 0.037 0.002 TYR B 904 ARG 0.012 0.001 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 385 time to evaluate : 3.424 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 464 PHE cc_start: 0.8746 (m-80) cc_final: 0.8435 (m-80) REVERT: A 784 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8676 (mm-40) REVERT: A 984 LEU cc_start: 0.7943 (tp) cc_final: 0.7720 (tp) REVERT: L 24 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7623 (mmm160) REVERT: B 140 PHE cc_start: 0.8826 (p90) cc_final: 0.8306 (p90) REVERT: B 784 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8696 (mt0) REVERT: B 1138 TYR cc_start: 0.7882 (t80) cc_final: 0.7672 (t80) REVERT: C 36 TRP cc_start: 0.7366 (m100) cc_final: 0.6169 (m100) REVERT: C 58 MET cc_start: 0.6333 (ttp) cc_final: 0.6131 (ttp) REVERT: C 61 GLN cc_start: 0.7739 (tp40) cc_final: 0.7074 (pp30) REVERT: E 442 ASP cc_start: 0.6006 (m-30) cc_final: 0.5720 (m-30) REVERT: E 565 PHE cc_start: 0.7130 (t80) cc_final: 0.6840 (t80) REVERT: F 61 GLN cc_start: 0.7722 (tp40) cc_final: 0.7104 (pp30) REVERT: G 14 SER cc_start: 0.7375 (m) cc_final: 0.6898 (p) outliers start: 85 outliers final: 54 residues processed: 432 average time/residue: 0.4289 time to fit residues: 293.8824 Evaluate side-chains 389 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 333 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 353 optimal weight: 0.5980 chunk 374 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 762 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 755 GLN B 762 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E1142 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31611 Z= 0.214 Angle : 0.592 9.134 43014 Z= 0.313 Chirality : 0.046 0.307 4983 Planarity : 0.004 0.041 5499 Dihedral : 5.373 36.013 5130 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.52 % Allowed : 9.80 % Favored : 87.69 % 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: 0.05 (0.13), residues: 3837 helix: 1.92 (0.20), residues: 663 sheet: 0.10 (0.15), residues: 1113 loop : -0.61 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 35 HIS 0.015 0.001 HIS B 245 PHE 0.027 0.002 PHE B 497 TYR 0.021 0.002 TYR C 32 ARG 0.008 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 368 time to evaluate : 3.702 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: A 226 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 335 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7267 (tt) REVERT: L 24 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7452 (tpt170) REVERT: B 140 PHE cc_start: 0.8856 (p90) cc_final: 0.8261 (p90) REVERT: B 226 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7380 (mp) REVERT: B 1138 TYR cc_start: 0.7952 (t80) cc_final: 0.7743 (t80) REVERT: C 36 TRP cc_start: 0.7282 (m100) cc_final: 0.6338 (m100) REVERT: C 61 GLN cc_start: 0.7835 (tp40) cc_final: 0.7274 (pp30) REVERT: E 442 ASP cc_start: 0.6013 (m-30) cc_final: 0.5741 (m-30) REVERT: F 36 TRP cc_start: 0.7628 (m100) cc_final: 0.7181 (m100) REVERT: F 61 GLN cc_start: 0.7721 (tp40) cc_final: 0.7233 (pp30) REVERT: G 4 MET cc_start: 0.4652 (tmm) cc_final: 0.4118 (tmm) REVERT: G 14 SER cc_start: 0.7372 (m) cc_final: 0.6886 (p) outliers start: 85 outliers final: 57 residues processed: 410 average time/residue: 0.4208 time to fit residues: 276.6287 Evaluate side-chains 396 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 336 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain E residue 1141 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 278 optimal weight: 0.0070 chunk 154 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 GLN E 762 GLN E 913 GLN E1005 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31611 Z= 0.184 Angle : 0.567 10.064 43014 Z= 0.299 Chirality : 0.045 0.301 4983 Planarity : 0.004 0.042 5499 Dihedral : 5.162 35.626 5130 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 2.78 % Allowed : 10.36 % Favored : 86.86 % 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: 0.07 (0.13), residues: 3837 helix: 2.27 (0.20), residues: 645 sheet: 0.04 (0.15), residues: 1113 loop : -0.65 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 35 HIS 0.005 0.001 HIS A 245 PHE 0.021 0.002 PHE H 29 TYR 0.025 0.001 TYR C 32 ARG 0.008 0.000 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 352 time to evaluate : 3.554 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: A 226 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7285 (mp) REVERT: A 335 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7376 (tt) REVERT: A 449 TYR cc_start: 0.7970 (m-80) cc_final: 0.7666 (m-80) REVERT: H 23 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8237 (mttt) REVERT: H 80 MET cc_start: 0.6013 (tmm) cc_final: 0.5456 (tmm) REVERT: L 24 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7273 (tpt90) REVERT: B 140 PHE cc_start: 0.8858 (p90) cc_final: 0.8294 (p90) REVERT: C 36 TRP cc_start: 0.7241 (m100) cc_final: 0.6379 (m100) REVERT: C 61 GLN cc_start: 0.7897 (tp40) cc_final: 0.7370 (pp30) REVERT: E 376 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8490 (p) REVERT: E 442 ASP cc_start: 0.6070 (m-30) cc_final: 0.5837 (m-30) REVERT: F 61 GLN cc_start: 0.7654 (tp40) cc_final: 0.7221 (pp30) REVERT: G 4 MET cc_start: 0.4616 (tmm) cc_final: 0.4088 (tmm) REVERT: G 14 SER cc_start: 0.7360 (m) cc_final: 0.6896 (p) outliers start: 94 outliers final: 66 residues processed: 405 average time/residue: 0.4034 time to fit residues: 264.6360 Evaluate side-chains 396 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 327 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 310 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 196 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 762 GLN B 804 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 31611 Z= 0.517 Angle : 0.703 10.752 43014 Z= 0.366 Chirality : 0.049 0.313 4983 Planarity : 0.005 0.042 5499 Dihedral : 5.675 42.666 5130 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 3.26 % Allowed : 10.39 % Favored : 86.35 % 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: -0.33 (0.13), residues: 3837 helix: 1.82 (0.20), residues: 642 sheet: -0.17 (0.15), residues: 1128 loop : -0.90 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 35 HIS 0.008 0.001 HIS B1058 PHE 0.025 0.003 PHE A 898 TYR 0.037 0.002 TYR B 351 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 341 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 449 TYR cc_start: 0.7981 (m-80) cc_final: 0.7736 (m-80) REVERT: A 571 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6499 (t0) REVERT: A 984 LEU cc_start: 0.7905 (tp) cc_final: 0.7501 (tt) REVERT: H 23 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8223 (mttt) REVERT: H 80 MET cc_start: 0.6131 (tmm) cc_final: 0.5652 (tmm) REVERT: B 140 PHE cc_start: 0.8933 (p90) cc_final: 0.8263 (p90) REVERT: B 784 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8860 (mt0) REVERT: C 36 TRP cc_start: 0.7239 (m100) cc_final: 0.6321 (m100) REVERT: C 61 GLN cc_start: 0.8078 (tp40) cc_final: 0.7336 (pp30) REVERT: C 100 PHE cc_start: 0.7003 (m-80) cc_final: 0.6690 (m-10) REVERT: E 376 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8504 (p) REVERT: E 571 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6312 (t0) REVERT: F 61 GLN cc_start: 0.7700 (tp40) cc_final: 0.7187 (pp30) REVERT: F 66 ARG cc_start: 0.6846 (mtm110) cc_final: 0.6605 (ttm110) REVERT: G 4 MET cc_start: 0.4546 (tmm) cc_final: 0.3943 (tmm) REVERT: G 14 SER cc_start: 0.7122 (m) cc_final: 0.6685 (p) outliers start: 110 outliers final: 82 residues processed: 408 average time/residue: 0.4033 time to fit residues: 267.2398 Evaluate side-chains 405 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 318 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 90 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 994 ASP Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 315 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 373 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 762 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 31611 Z= 0.201 Angle : 0.591 11.976 43014 Z= 0.306 Chirality : 0.045 0.289 4983 Planarity : 0.004 0.057 5499 Dihedral : 5.308 41.755 5130 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 2.78 % Allowed : 11.22 % Favored : 86.00 % 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: -0.25 (0.14), residues: 3837 helix: 2.07 (0.20), residues: 669 sheet: -0.25 (0.15), residues: 1176 loop : -0.87 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 35 HIS 0.023 0.001 HIS B 245 PHE 0.026 0.002 PHE E 565 TYR 0.030 0.002 TYR B 351 ARG 0.007 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 343 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 335 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 739 THR cc_start: 0.8772 (m) cc_final: 0.8458 (p) REVERT: A 957 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 979 ASP cc_start: 0.7890 (t0) cc_final: 0.7690 (t0) REVERT: A 1005 GLN cc_start: 0.7672 (tt0) cc_final: 0.7382 (mt0) REVERT: H 80 MET cc_start: 0.5889 (tmm) cc_final: 0.5325 (tmm) REVERT: L 48 ILE cc_start: 0.5434 (OUTLIER) cc_final: 0.5092 (mm) REVERT: B 140 PHE cc_start: 0.8887 (p90) cc_final: 0.8326 (p90) REVERT: B 634 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7839 (mtm-85) REVERT: B 784 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: C 36 TRP cc_start: 0.7190 (m100) cc_final: 0.6319 (m100) REVERT: C 47 TRP cc_start: 0.6704 (t60) cc_final: 0.6299 (t60) REVERT: C 61 GLN cc_start: 0.8003 (tp40) cc_final: 0.7421 (pp30) REVERT: E 376 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8486 (p) REVERT: F 61 GLN cc_start: 0.7640 (tp40) cc_final: 0.7248 (pp30) REVERT: G 4 MET cc_start: 0.4601 (tmm) cc_final: 0.4003 (tmm) REVERT: G 14 SER cc_start: 0.7090 (m) cc_final: 0.6681 (p) outliers start: 94 outliers final: 69 residues processed: 396 average time/residue: 0.4015 time to fit residues: 257.9486 Evaluate side-chains 389 residues out of total 3378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 315 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 90 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 63.7613 > 50: distance: 46 - 81: 27.947 distance: 49 - 78: 28.662 distance: 68 - 73: 29.399 distance: 73 - 74: 41.060 distance: 74 - 75: 21.866 distance: 74 - 77: 10.098 distance: 75 - 76: 3.996 distance: 75 - 78: 11.856 distance: 76 - 247: 24.902 distance: 78 - 79: 30.667 distance: 79 - 80: 19.347 distance: 79 - 82: 27.716 distance: 80 - 81: 4.273 distance: 80 - 88: 18.374 distance: 82 - 83: 12.568 distance: 83 - 84: 31.216 distance: 83 - 85: 4.606 distance: 84 - 86: 13.203 distance: 85 - 87: 9.502 distance: 86 - 87: 19.853 distance: 88 - 89: 15.835 distance: 88 - 232: 17.033 distance: 89 - 90: 30.892 distance: 89 - 92: 16.546 distance: 90 - 91: 45.534 distance: 90 - 99: 49.707 distance: 91 - 229: 31.795 distance: 92 - 93: 15.095 distance: 93 - 94: 29.978 distance: 93 - 95: 27.768 distance: 94 - 96: 22.423 distance: 95 - 97: 27.690 distance: 97 - 98: 43.504 distance: 99 - 100: 50.122 distance: 99 - 105: 46.717 distance: 100 - 101: 24.881 distance: 100 - 103: 31.707 distance: 101 - 102: 13.951 distance: 101 - 106: 30.031 distance: 103 - 104: 21.453 distance: 104 - 105: 23.012 distance: 106 - 107: 10.811 distance: 107 - 108: 24.647 distance: 107 - 110: 17.462 distance: 108 - 109: 20.663 distance: 108 - 117: 17.399 distance: 110 - 111: 15.675 distance: 111 - 112: 11.460 distance: 113 - 114: 5.540 distance: 114 - 115: 7.984 distance: 114 - 116: 4.875 distance: 117 - 118: 16.093 distance: 118 - 119: 21.788 distance: 118 - 121: 29.810 distance: 119 - 120: 33.449 distance: 119 - 126: 36.065 distance: 121 - 122: 29.702 distance: 123 - 124: 9.456 distance: 123 - 125: 17.249 distance: 126 - 127: 25.714 distance: 127 - 128: 46.401 distance: 128 - 129: 44.653 distance: 128 - 130: 36.352 distance: 130 - 131: 18.760 distance: 130 - 190: 27.204 distance: 131 - 132: 34.682 distance: 131 - 134: 13.231 distance: 132 - 133: 42.178 distance: 132 - 137: 11.903 distance: 133 - 187: 32.413 distance: 134 - 135: 20.551 distance: 134 - 136: 6.276 distance: 137 - 138: 19.227 distance: 138 - 139: 25.756 distance: 138 - 141: 15.197 distance: 139 - 140: 22.165 distance: 139 - 148: 12.226 distance: 141 - 142: 13.791 distance: 142 - 143: 24.514 distance: 142 - 144: 11.676 distance: 143 - 145: 17.891 distance: 144 - 146: 15.246 distance: 145 - 147: 5.000 distance: 146 - 147: 13.195 distance: 148 - 149: 18.837 distance: 148 - 176: 15.746 distance: 149 - 150: 27.603 distance: 149 - 152: 7.672 distance: 150 - 151: 41.146 distance: 150 - 155: 12.110 distance: 151 - 173: 33.216 distance: 152 - 153: 31.201 distance: 152 - 154: 9.640