Starting phenix.real_space_refine on Wed Mar 20 23:07:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru5_24697/03_2024/7ru5_24697.pdb" } resolution = 3.6 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= 0.023 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 138 5.16 5 C 18216 2.51 5 N 4734 2.21 5 O 5585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28673 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 8527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8527 Classifications: {'peptide': 1093} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "F" 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: "G" 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: "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: "C" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 Time building chain proxies: 14.72, per 1000 atoms: 0.51 Number of scatterers: 28673 At special positions: 0 Unit cell: (146.26, 151.41, 229.69, 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 138 16.00 O 5585 8.00 N 4734 7.00 C 18216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.12 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.05 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 148 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 5.4 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 64 sheets defined 23.7% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.484A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 removed outlier: 4.091A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.785A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.647A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.550A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.536A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 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 967 removed outlier: 3.980A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.139A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.122A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.423A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.438A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.894A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.936A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.773A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.782A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.479A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.807A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.798A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AC2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.698A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.993A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.565A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.207A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.427A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.541A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.325A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.763A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.616A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.563A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.380A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.971A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.951A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.631A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AE9, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.100A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.795A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.790A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.810A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 59 removed outlier: 5.758A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 96 through 100 Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.284A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 48 through 49 1231 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.87 Time building geometry restraints manager: 13.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5423 1.32 - 1.46: 10892 1.46 - 1.61: 12804 1.61 - 1.76: 38 1.76 - 1.91: 152 Bond restraints: 29309 Sorted by residual: bond pdb=" CB LEU B 387 " pdb=" CG LEU B 387 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB HIS C1048 " pdb=" CG HIS C1048 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" CB LEU A 387 " pdb=" CG LEU A 387 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CB HIS C1064 " pdb=" CG HIS C1064 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" NE ARG L 96 " pdb=" CZ ARG L 96 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 3.02e+01 ... (remaining 29304 not shown) Histogram of bond angle deviations from ideal: 95.47 - 108.73: 3663 108.73 - 121.99: 30224 121.99 - 135.25: 5967 135.25 - 148.51: 0 148.51 - 161.77: 1 Bond angle restraints: 39855 Sorted by residual: angle pdb=" C2 NAG B1303 " pdb=" N2 NAG B1303 " pdb=" C7 NAG B1303 " ideal model delta sigma weight residual 124.56 161.77 -37.21 3.00e+00 1.11e-01 1.54e+02 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 110.82 100.29 10.53 9.70e-01 1.06e+00 1.18e+02 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 122.96 -10.36 1.00e+00 1.00e+00 1.07e+02 angle pdb=" N ARG D 94 " pdb=" CA ARG D 94 " pdb=" C ARG D 94 " ideal model delta sigma weight residual 113.17 125.10 -11.93 1.26e+00 6.30e-01 8.96e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 124.80 -11.63 1.26e+00 6.30e-01 8.52e+01 ... (remaining 39850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17379 17.96 - 35.92: 426 35.92 - 53.88: 140 53.88 - 71.84: 52 71.84 - 89.80: 24 Dihedral angle restraints: 18021 sinusoidal: 7540 harmonic: 10481 Sorted by residual: dihedral pdb=" CB CYS C 705 " pdb=" SG CYS C 705 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 174.27 -81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.90 -71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 160.91 -67.91 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 18018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3336 0.107 - 0.214: 992 0.214 - 0.321: 211 0.321 - 0.428: 61 0.428 - 0.535: 23 Chirality restraints: 4623 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4620 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.089 2.00e-02 2.50e+03 9.47e-02 1.12e+02 pdb=" CG ASN A 616 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.148 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.065 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" CG ASN A 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " 0.055 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 616 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 12127 2.91 - 3.41: 27104 3.41 - 3.91: 50650 3.91 - 4.40: 58477 4.40 - 4.90: 92068 Nonbonded interactions: 240426 Sorted by model distance: nonbonded pdb=" N ASN C 149 " pdb=" N LYS C 150 " model vdw 2.413 2.560 nonbonded pdb=" N ASP A1084 " pdb=" OD1 ASP A1084 " model vdw 2.430 2.520 nonbonded pdb=" N ARG C 44 " pdb=" O ARG C 44 " model vdw 2.440 2.496 nonbonded pdb=" O GLN B 498 " pdb=" ND2 ASN B 501 " model vdw 2.440 2.520 nonbonded pdb=" N ASP A 111 " pdb=" OD1 ASP A 111 " model vdw 2.449 2.520 ... (remaining 240421 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' and (resid 14 through 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 260 or resid 263 through 387 or resid 395 through 426 \ or resid 429 through 515 or resid 522 through 637 or resid 641 through 827 or re \ sid 848 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 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: 20.110 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 81.570 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 0.128 29309 Z= 1.308 Angle : 1.818 37.211 39855 Z= 1.223 Chirality : 0.115 0.535 4623 Planarity : 0.009 0.047 5102 Dihedral : 10.142 89.802 11129 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.47 (0.13), residues: 3545 helix: 0.68 (0.17), residues: 704 sheet: 0.90 (0.18), residues: 764 loop : 0.04 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.012 TRP H 47 HIS 0.012 0.002 HIS B1048 PHE 0.060 0.007 PHE B 342 TYR 0.083 0.010 TYR A 489 ARG 0.010 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 3.312 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: C 740 MET cc_start: 0.9210 (mtp) cc_final: 0.8941 (mtt) REVERT: C 780 GLU cc_start: 0.8537 (tp30) cc_final: 0.8150 (tp30) REVERT: A 140 PHE cc_start: 0.6808 (m-80) cc_final: 0.6534 (m-80) REVERT: A 153 MET cc_start: 0.7288 (ttp) cc_final: 0.5117 (ptt) REVERT: B 731 MET cc_start: 0.8820 (ttp) cc_final: 0.8613 (ttm) REVERT: H 36 TRP cc_start: 0.6112 (m100) cc_final: 0.4867 (m100) REVERT: H 47 TRP cc_start: 0.4745 (t60) cc_final: 0.3767 (t60) REVERT: H 63 PHE cc_start: 0.6224 (m-80) cc_final: 0.5684 (m-80) REVERT: H 100 TYR cc_start: 0.4997 (m-80) cc_final: 0.4685 (m-80) REVERT: H 100 PHE cc_start: 0.6485 (m-10) cc_final: 0.5639 (m-80) REVERT: D 82 LEU cc_start: 0.3850 (mt) cc_final: 0.3170 (mp) REVERT: E 48 ILE cc_start: 0.9026 (mt) cc_final: 0.8506 (mp) REVERT: E 98 PHE cc_start: 0.0354 (m-80) cc_final: -0.0030 (m-80) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.4567 time to fit residues: 105.4138 Evaluate side-chains 92 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 324 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 914 ASN C 955 ASN A 321 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN L 37 GLN D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29309 Z= 0.221 Angle : 0.657 7.132 39855 Z= 0.360 Chirality : 0.046 0.342 4623 Planarity : 0.005 0.072 5102 Dihedral : 5.672 40.546 4706 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.57 % Allowed : 2.45 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.60 (0.13), residues: 3545 helix: 2.28 (0.19), residues: 712 sheet: 0.54 (0.18), residues: 803 loop : -0.32 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 100G HIS 0.004 0.001 HIS C 655 PHE 0.028 0.002 PHE L 62 TYR 0.028 0.002 TYR D 98 ARG 0.009 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 3.341 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: C 740 MET cc_start: 0.9049 (mtp) cc_final: 0.8688 (mtt) REVERT: A 140 PHE cc_start: 0.6494 (m-80) cc_final: 0.6203 (m-80) REVERT: A 153 MET cc_start: 0.7481 (ttp) cc_final: 0.6877 (tpp) REVERT: A 731 MET cc_start: 0.8901 (ttm) cc_final: 0.8658 (ttm) REVERT: B 731 MET cc_start: 0.8632 (ttp) cc_final: 0.8360 (ttm) REVERT: H 47 TRP cc_start: 0.4584 (t60) cc_final: 0.3703 (t60) REVERT: H 62 LYS cc_start: 0.5106 (tptp) cc_final: 0.4677 (tmtt) REVERT: H 63 PHE cc_start: 0.6265 (m-80) cc_final: 0.5758 (m-80) REVERT: H 100 TYR cc_start: 0.5374 (m-80) cc_final: 0.4990 (m-80) REVERT: D 80 MET cc_start: -0.0354 (ttp) cc_final: -0.1156 (ttp) REVERT: D 82 LEU cc_start: 0.3912 (mt) cc_final: 0.3149 (tp) REVERT: D 98 TYR cc_start: 0.8524 (m-80) cc_final: 0.8051 (m-80) REVERT: E 98 PHE cc_start: 0.0420 (m-80) cc_final: 0.0164 (m-10) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 0.3986 time to fit residues: 84.2385 Evaluate side-chains 98 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 324 optimal weight: 30.0000 chunk 350 optimal weight: 30.0000 chunk 289 optimal weight: 2.9990 chunk 322 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 314 GLN C 519 HIS C 613 GLN A 655 HIS A 914 ASN B 207 HIS B 487 ASN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 29309 Z= 0.373 Angle : 0.682 9.510 39855 Z= 0.357 Chirality : 0.046 0.334 4623 Planarity : 0.004 0.042 5102 Dihedral : 5.475 54.380 4706 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.60 % Allowed : 3.56 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.24 (0.13), residues: 3545 helix: 2.45 (0.19), residues: 710 sheet: 0.02 (0.17), residues: 909 loop : -0.64 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.009 0.002 HIS B 655 PHE 0.029 0.002 PHE H 100F TYR 0.025 0.002 TYR A1067 ARG 0.009 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 3.182 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 140 PHE cc_start: 0.6659 (m-80) cc_final: 0.6293 (m-80) REVERT: A 153 MET cc_start: 0.7882 (ttp) cc_final: 0.7393 (tpp) REVERT: B 731 MET cc_start: 0.8937 (ttp) cc_final: 0.8641 (ttm) REVERT: H 46 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6710 (mt-10) REVERT: H 47 TRP cc_start: 0.4772 (t60) cc_final: 0.4422 (t60) REVERT: L 73 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6617 (tt) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.4055 time to fit residues: 75.9329 Evaluate side-chains 96 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 2.9990 chunk 244 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 chunk 345 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 308 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN C 655 HIS C 913 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN A1002 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 29309 Z= 0.415 Angle : 0.669 9.997 39855 Z= 0.349 Chirality : 0.046 0.328 4623 Planarity : 0.004 0.043 5102 Dihedral : 5.517 53.158 4706 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.92 % Allowed : 4.48 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.04 (0.14), residues: 3545 helix: 2.47 (0.19), residues: 695 sheet: -0.14 (0.17), residues: 881 loop : -0.80 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 35 HIS 0.007 0.002 HIS C1048 PHE 0.036 0.002 PHE B 906 TYR 0.023 0.002 TYR B1067 ARG 0.008 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 3.221 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: C 177 MET cc_start: 0.4770 (tmm) cc_final: 0.4424 (tmm) REVERT: A 153 MET cc_start: 0.7878 (ttp) cc_final: 0.7479 (tpp) REVERT: A 900 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: A 912 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 731 MET cc_start: 0.8991 (ttp) cc_final: 0.8725 (ttm) REVERT: H 46 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6586 (mt-10) REVERT: H 47 TRP cc_start: 0.5280 (t60) cc_final: 0.4924 (t60) REVERT: L 47 LEU cc_start: 0.5405 (tt) cc_final: 0.5067 (tp) REVERT: L 73 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6414 (tt) outliers start: 29 outliers final: 21 residues processed: 111 average time/residue: 0.4207 time to fit residues: 80.2493 Evaluate side-chains 108 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 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: 52.7862 > 50: distance: 13 - 143: 16.489 distance: 16 - 140: 21.575 distance: 69 - 73: 5.510 distance: 73 - 74: 15.380 distance: 74 - 75: 6.956 distance: 75 - 76: 13.542 distance: 75 - 77: 9.322 distance: 77 - 78: 10.069 distance: 78 - 79: 18.383 distance: 78 - 81: 17.547 distance: 79 - 80: 10.295 distance: 79 - 84: 7.272 distance: 81 - 82: 18.725 distance: 81 - 83: 21.600 distance: 84 - 85: 5.407 distance: 85 - 86: 16.228 distance: 85 - 88: 10.393 distance: 86 - 87: 10.009 distance: 86 - 90: 11.367 distance: 87 - 104: 22.392 distance: 88 - 89: 22.386 distance: 90 - 91: 10.764 distance: 90 - 96: 11.841 distance: 91 - 92: 15.567 distance: 91 - 94: 7.212 distance: 92 - 93: 9.905 distance: 92 - 97: 11.306 distance: 93 - 113: 15.957 distance: 94 - 95: 6.915 distance: 95 - 96: 22.462 distance: 97 - 98: 11.017 distance: 98 - 99: 11.431 distance: 98 - 101: 10.637 distance: 99 - 100: 12.783 distance: 99 - 104: 9.135 distance: 101 - 102: 19.475 distance: 101 - 103: 5.673 distance: 104 - 105: 6.940 distance: 105 - 106: 13.702 distance: 105 - 108: 16.762 distance: 106 - 113: 10.523 distance: 108 - 109: 15.371 distance: 109 - 110: 13.034 distance: 110 - 111: 11.074 distance: 111 - 112: 7.146 distance: 113 - 114: 6.130 distance: 114 - 115: 9.493 distance: 114 - 117: 8.660 distance: 115 - 116: 10.796 distance: 117 - 118: 7.167 distance: 118 - 119: 15.226 distance: 118 - 120: 10.572 distance: 121 - 122: 16.607 distance: 122 - 123: 9.208 distance: 122 - 125: 15.729 distance: 123 - 124: 13.610 distance: 123 - 128: 9.736 distance: 125 - 126: 8.093 distance: 125 - 127: 13.117 distance: 128 - 129: 11.058 distance: 128 - 174: 6.884 distance: 129 - 130: 12.771 distance: 129 - 132: 18.474 distance: 130 - 131: 43.067 distance: 130 - 140: 15.707 distance: 131 - 171: 32.885 distance: 132 - 133: 11.439 distance: 133 - 134: 13.707 distance: 133 - 135: 16.982 distance: 134 - 136: 18.013 distance: 135 - 137: 13.009 distance: 136 - 138: 6.854 distance: 137 - 138: 8.998 distance: 138 - 139: 7.102 distance: 140 - 141: 19.404 distance: 141 - 142: 7.399 distance: 141 - 144: 14.746 distance: 142 - 143: 15.115