Starting phenix.real_space_refine (version: 1.20rc2) on Thu Nov 4 21:11:28 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/11_2021/7s0d_24787.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 151": "OD1" <-> "OD2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 28": "OD1" <-> "OD2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 28": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc2-4405/modules/chem_data/mon_lib" Total number of atoms: 33623 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7844 Classifications: {'peptide': 1013} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 54, 'TRANS': 958} Chain breaks: 9 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 7976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7976 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 55, 'TRANS': 977} Chain breaks: 10 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7882 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 54, 'TRANS': 971} Chain breaks: 10 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "H" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 211, 'PCIS': 2} Chain: "L" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} bond proxies already assigned to first conformer: 1678 Chain: "M" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 211, 'PCIS': 2} Chain: "N" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} bond proxies already assigned to first conformer: 1678 Chain: "O" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 211, 'PCIS': 2} Chain: "P" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 9, 'TRANS': 202, 'PCIS': 2} bond proxies already assigned to first conformer: 1678 Time building chain proxies: 21.99, per 1000 atoms: 0.65 Number of scatterers: 33623 At special positions: 0 Unit cell: (239.844, 231.154, 181.621, 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 149 16.00 O 6482 8.00 N 5604 7.00 C 21388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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 A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 148 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG ACYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG BCYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 148 " - pdb=" SG CYS O 204 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG ACYS P 194 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG BCYS P 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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 Time building additional restraints: 14.96 Conformation dependent library (CDL) restraints added in 6.1 seconds 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8200 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 73 sheets defined 19.6% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.634A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.488A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.926A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.775A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.317A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (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 removed outlier: 3.734A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.301A 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 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 removed outlier: 3.920A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.903A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.545A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.513A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) 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 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.174A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.568A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.548A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.607A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.563A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.293A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.668A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) 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 755 removed outlier: 4.445A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.081A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.384A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.197A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.697A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.472A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.287A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'L' and resid 121 through 127 removed outlier: 4.085A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.685A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'N' and resid 121 through 128 removed outlier: 4.216A pdb=" N SER N 127 " --> pdb=" O GLU N 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 188 Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.713A pdb=" N THR O 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'P' and resid 121 through 127 removed outlier: 4.072A pdb=" N SER P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.437A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.514A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.249A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 10.597A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.625A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.358A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.498A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.723A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.102A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.563A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.585A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.496A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.063A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 10.726A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.669A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 8.723A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.280A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.776A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.897A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.680A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.786A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 727 removed outlier: 6.350A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 727 Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.398A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.978A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 10.661A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.627A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.428A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.965A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.801A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.959A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.959A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.237A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.623A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.357A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.234A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.234A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 185 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 177 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 158 through 159 removed outlier: 3.529A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.991A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.630A pdb=" N PHE L 116 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR L 172 " --> pdb=" O GLN L 166 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN L 166 " --> pdb=" O THR L 172 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.910A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 197 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.790A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.733A pdb=" N VAL M 12 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.840A pdb=" N GLY M 147 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR M 184 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.840A pdb=" N GLY M 147 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR M 184 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 158 through 162 Processing sheet with id=AG7, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.196A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA N 13 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 19 through 20 removed outlier: 3.581A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.798A pdb=" N PHE N 116 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 130 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR N 172 " --> pdb=" O GLN N 166 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN N 166 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER N 174 " --> pdb=" O THR N 164 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 153 through 154 removed outlier: 3.888A pdb=" N LYS N 145 " --> pdb=" O THR N 197 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.762A pdb=" N LEU O 18 " --> pdb=" O MET O 83 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N VAL O 12 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 128 through 131 removed outlier: 5.067A pdb=" N ALA O 145 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL O 192 " --> pdb=" O ALA O 145 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLY O 147 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL O 190 " --> pdb=" O GLY O 147 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU O 149 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER O 188 " --> pdb=" O LEU O 149 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS O 151 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU O 186 " --> pdb=" O LYS O 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR O 153 " --> pdb=" O TYR O 184 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 158 through 162 Processing sheet with id=AH7, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH8, first strand: chain 'P' and resid 10 through 14 removed outlier: 4.149A pdb=" N LEU P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU P 105 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.633A pdb=" N PHE P 116 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL P 132 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER P 177 " --> pdb=" O CYS P 134 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU P 136 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU P 175 " --> pdb=" O LEU P 136 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR P 172 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN P 166 " --> pdb=" O THR P 172 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER P 174 " --> pdb=" O THR P 164 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 153 through 154 removed outlier: 3.589A pdb=" N TYR P 192 " --> pdb=" O PHE P 209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS P 207 " --> pdb=" O CYS P 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL P 196 " --> pdb=" O VAL P 205 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 205 " --> pdb=" O VAL P 196 " (cutoff:3.500A) 1333 hydrogen bonds defined for protein. 3546 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: 17.55 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10831 1.35 - 1.48: 8984 1.48 - 1.61: 14389 1.61 - 1.75: 7 1.75 - 1.88: 183 Bond restraints: 34394 Sorted by residual: bond pdb=" N PRO P 40 " pdb=" CD PRO P 40 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.22e+01 bond pdb=" CB PRO P 40 " pdb=" CG PRO P 40 " ideal model delta sigma weight residual 1.492 1.657 -0.165 5.00e-02 4.00e+02 1.09e+01 bond pdb=" CB PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 1.492 1.629 -0.137 5.00e-02 4.00e+02 7.48e+00 bond pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.12e+00 bond pdb=" C LEU P 78 " pdb=" N GLN P 79 " ideal model delta sigma weight residual 1.339 1.472 -0.132 5.57e-02 3.22e+02 5.64e+00 ... (remaining 34389 not shown) Histogram of bond angle deviations from ideal: 95.21 - 104.02: 545 104.02 - 112.83: 18392 112.83 - 121.64: 19492 121.64 - 130.45: 8318 130.45 - 139.26: 107 Bond angle restraints: 46854 Sorted by residual: angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 139.26 -24.86 2.30e+00 1.89e-01 1.17e+02 angle pdb=" CA PRO P 40 " pdb=" N PRO P 40 " pdb=" CD PRO P 40 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.77e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.04 -13.64 2.30e+00 1.89e-01 3.52e+01 angle pdb=" CA PRO N 80 " pdb=" N PRO N 80 " pdb=" CD PRO N 80 " ideal model delta sigma weight residual 112.00 104.08 7.92 1.40e+00 5.10e-01 3.20e+01 ... (remaining 46849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 18772 17.93 - 35.87: 1375 35.87 - 53.80: 284 53.80 - 71.73: 56 71.73 - 89.67: 34 Dihedral angle restraints: 20521 sinusoidal: 7782 harmonic: 12739 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -170.90 84.90 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -14.70 -71.30 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.52 -66.52 1 1.00e+01 1.00e-02 5.77e+01 ... (remaining 20518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5065 0.106 - 0.212: 280 0.212 - 0.317: 11 0.317 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 5359 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 5356 not shown) Planarity restraints: 6046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 79 " 0.111 5.00e-02 4.00e+02 1.63e-01 4.28e+01 pdb=" N PRO N 80 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO N 80 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO N 80 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 101 " 0.044 2.00e-02 2.50e+03 3.70e-02 3.43e+01 pdb=" CG TRP H 101 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP H 101 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP H 101 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 101 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 101 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS P 39 " -0.102 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO P 40 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO P 40 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO P 40 " -0.074 5.00e-02 4.00e+02 ... (remaining 6043 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 285 2.56 - 3.14: 27733 3.14 - 3.73: 51229 3.73 - 4.31: 70402 4.31 - 4.90: 117112 Nonbonded interactions: 266761 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 1.969 2.440 nonbonded pdb=" O GLN A 755 " pdb=" OG SER C 968 " model vdw 2.020 2.440 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.044 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN C 394 " model vdw 2.063 2.520 nonbonded pdb=" O ILE A 101 " pdb=" NH2 ARG A 190 " model vdw 2.072 2.520 ... (remaining 266756 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' and (resid 14 through 331 or (resid 332 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 344 or (resid 345 t \ hrough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 363 or (resid 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 373 or (res \ id 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thr \ ough 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 504 or (res \ id 505 and (name N or name CA or name C or name O or name CB )) or resid 506 thr \ ough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1146)) selection = (chain 'B' and (resid 14 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 426 or (resid 427 t \ hrough 428 and (name N or name CA or name C or name O or name CB )) or resid 429 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or resi \ d 503 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 throu \ gh 1146)) selection = (chain 'C' and (resid 14 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 454 or resid 491 th \ rough 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) \ or resid 506 through 1146)) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'N' and (resid 1 through 193 or resid 195 through 214)) selection = (chain 'P' and (resid 1 through 193 or resid 195 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 149 5.16 5 C 21388 2.51 5 N 5604 2.21 5 O 6482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.04 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 Write .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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.260 Check model and map are aligned: 0.580 Convert atoms to be neutral: 0.310 Process input model: 95.380 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 125.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.005 0.165 34394 Z= 0.300 Angle : 0.882 24.864 46854 Z= 0.476 Chirality : 0.053 0.529 5359 Planarity : 0.007 0.163 6046 Dihedral : 13.461 89.667 12159 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.01 % Favored : 93.36 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.26 % 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: -0.74 (0.13), residues: 4310 helix: 1.05 (0.20), residues: 712 sheet: -0.10 (0.15), residues: 1110 loop : -1.16 (0.12), residues: 2488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 459 time to evaluate : 4.257 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 outliers start: 5 outliers final: 0 residues processed: 461 average time/residue: 0.4359 time to fit residues: 333.9201 Evaluate side-chains 271 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.699 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 253 optimal weight: 0.0040 chunk 395 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 755 GLN B1002 GLN B1106 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1088 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS H 205 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN P 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 34394 Z= 0.313 Angle : 0.698 15.875 46854 Z= 0.368 Chirality : 0.047 0.217 5359 Planarity : 0.006 0.112 6046 Dihedral : 5.252 24.771 4667 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.62 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.67 (0.13), residues: 4310 helix: 1.02 (0.20), residues: 705 sheet: -0.17 (0.15), residues: 1116 loop : -1.01 (0.12), residues: 2489 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 325 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 43 residues processed: 372 average time/residue: 0.4337 time to fit residues: 268.4150 Evaluate side-chains 302 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 259 time to evaluate : 4.085 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3210 time to fit residues: 31.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 0.0970 chunk 268 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 395 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 392 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 317 optimal weight: 0.2980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 360 ASN B 394 ASN B 422 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN H 3 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN H 172 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 ASN P 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 34394 Z= 0.191 Angle : 0.606 15.875 46854 Z= 0.317 Chirality : 0.044 0.225 5359 Planarity : 0.006 0.125 6046 Dihedral : 4.748 24.487 4667 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.11 % Favored : 94.68 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.13), residues: 4310 helix: 1.32 (0.20), residues: 704 sheet: -0.15 (0.15), residues: 1138 loop : -0.82 (0.12), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 303 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 329 average time/residue: 0.4449 time to fit residues: 246.0612 Evaluate side-chains 273 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 257 time to evaluate : 3.709 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3004 time to fit residues: 14.2650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 43 optimal weight: 0.0040 chunk 188 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 397 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS M 82 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN P 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.210 34394 Z= 0.272 Angle : 0.632 15.007 46854 Z= 0.334 Chirality : 0.045 0.274 5359 Planarity : 0.006 0.114 6046 Dihedral : 4.802 31.032 4667 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.94 % Favored : 93.87 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.45 (0.13), residues: 4310 helix: 1.25 (0.20), residues: 711 sheet: -0.23 (0.14), residues: 1214 loop : -0.78 (0.13), residues: 2385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 294 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 39 residues processed: 333 average time/residue: 0.4348 time to fit residues: 243.5594 Evaluate side-chains 287 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 3.637 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3287 time to fit residues: 28.0882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 0.0670 chunk 238 optimal weight: 0.9990 chunk 6 optimal weight: 0.0270 chunk 313 optimal weight: 6.9990 chunk 173 optimal weight: 0.0070 chunk 358 optimal weight: 8.9990 chunk 290 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 106 optimal weight: 0.0070 overall best weight: 0.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.562 34394 Z= 0.226 Angle : 0.753 73.900 46854 Z= 0.372 Chirality : 0.044 0.296 5359 Planarity : 0.006 0.119 6046 Dihedral : 4.716 34.789 4667 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.39 (0.13), residues: 4310 helix: 1.30 (0.20), residues: 711 sheet: -0.22 (0.14), residues: 1205 loop : -0.73 (0.13), residues: 2394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 281 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 16 residues processed: 320 average time/residue: 0.4563 time to fit residues: 248.1922 Evaluate side-chains 270 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 3.795 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5030 time to fit residues: 21.3055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 0.0870 chunk 420 optimal weight: 30.0000 chunk 349 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1108 ASN B 360 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.850 34394 Z= 0.512 Angle : 0.861 98.306 46854 Z= 0.435 Chirality : 0.046 0.659 5359 Planarity : 0.006 0.126 6046 Dihedral : 4.842 33.936 4667 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.36 % Favored : 93.45 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.49 (0.13), residues: 4310 helix: 1.24 (0.20), residues: 718 sheet: -0.27 (0.15), residues: 1171 loop : -0.81 (0.13), residues: 2421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 336 average time/residue: 0.4297 time to fit residues: 243.8966 Evaluate side-chains 280 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3158 time to fit residues: 26.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 307 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.141 34394 Z= 0.784 Angle : 1.094 95.828 46854 Z= 0.538 Chirality : 0.047 0.729 5359 Planarity : 0.007 0.161 6046 Dihedral : 4.895 34.590 4667 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.25 % Favored : 93.64 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.82 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.52 (0.13), residues: 4310 helix: 1.22 (0.20), residues: 718 sheet: -0.30 (0.15), residues: 1177 loop : -0.83 (0.13), residues: 2415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 269 average time/residue: 0.4509 time to fit residues: 207.5134 Evaluate side-chains 253 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 4.252 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3184 time to fit residues: 12.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 250 optimal weight: 0.6980 chunk 126 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.141 34394 Z= 0.884 Angle : 1.172 95.828 46854 Z= 0.611 Chirality : 0.047 0.729 5359 Planarity : 0.009 0.279 6046 Dihedral : 4.895 34.590 4667 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.25 % Favored : 93.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.82 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.02 % 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: -0.52 (0.13), residues: 4310 helix: 1.22 (0.20), residues: 718 sheet: -0.30 (0.15), residues: 1177 loop : -0.83 (0.13), residues: 2415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.4549 time to fit residues: 189.4886 Evaluate side-chains 241 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 4.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 3.9990 chunk 401 optimal weight: 0.8980 chunk 366 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 306 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 353 optimal weight: 3.9990 chunk 369 optimal weight: 8.9990 chunk 389 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.985 34394 Z= 0.649 Angle : 1.076 102.776 46854 Z= 0.522 Chirality : 0.046 0.704 5359 Planarity : 0.007 0.168 6046 Dihedral : 4.872 34.334 4667 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.50 (0.13), residues: 4310 helix: 1.29 (0.20), residues: 714 sheet: -0.24 (0.15), residues: 1155 loop : -0.85 (0.12), residues: 2441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 280 average time/residue: 0.4572 time to fit residues: 216.4909 Evaluate side-chains 262 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 4.177 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3150 time to fit residues: 15.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 433 optimal weight: 6.9990 chunk 398 optimal weight: 9.9990 chunk 345 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.971 34394 Z= 0.620 Angle : 1.060 99.838 46854 Z= 0.519 Chirality : 0.046 0.678 5359 Planarity : 0.007 0.175 6046 Dihedral : 4.855 35.306 4667 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.52 (0.13), residues: 4310 helix: 1.27 (0.20), residues: 718 sheet: -0.29 (0.15), residues: 1160 loop : -0.85 (0.13), residues: 2432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 256 average time/residue: 0.4525 time to fit residues: 195.3872 Evaluate side-chains 249 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 3.866 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4505 time to fit residues: 9.8616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 0.8980 chunk 367 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 345 optimal weight: 30.0000 chunk 144 optimal weight: 0.9990 chunk 354 optimal weight: 0.6980 chunk 43 optimal weight: 30.0000 chunk 63 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103117 restraints weight = 96871.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104723 restraints weight = 55510.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105027 restraints weight = 31066.467| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.972 34394 Z= 0.605 Angle : 1.035 98.929 46854 Z= 0.500 Chirality : 0.046 0.668 5359 Planarity : 0.007 0.180 6046 Dihedral : 4.837 34.914 4667 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.90 % Favored : 93.96 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.52 (0.13), residues: 4310 helix: 1.26 (0.20), residues: 719 sheet: -0.30 (0.15), residues: 1172 loop : -0.84 (0.13), residues: 2419 =============================================================================== Job complete usr+sys time: 6383.44 seconds wall clock time: 118 minutes 4.28 seconds (7084.28 seconds total)