Starting phenix.real_space_refine on Thu Feb 22 08:23:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/02_2024/7s0d_24787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/02_2024/7s0d_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_24787/02_2024/7s0d_24787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/02_2024/7s0d_24787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/02_2024/7s0d_24787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0d_24787/02_2024/7s0d_24787.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} 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: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "N" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} 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: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "P" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1678 Time building chain proxies: 18.86, per 1000 atoms: 0.56 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.62 Conformation dependent library (CDL) restraints added in 7.4 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: 4.18 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: 17.98 Time building geometry restraints manager: 13.71 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 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 Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.860 Check model and map are aligned: 0.710 Set scattering table: 0.300 Process input model: 94.750 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 18.32 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.01 % Favored : 93.36 % Rotamer: Outliers : 0.13 % Allowed : 0.62 % Favored : 99.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.004 TRP H 101 HIS 0.013 0.001 HIS B 66 PHE 0.033 0.002 PHE A 157 TYR 0.062 0.002 TYR P 186 ARG 0.018 0.001 ARG O 38 *********************** 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 : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8414 (mttt) cc_final: 0.8146 (mttt) REVERT: A 224 GLU cc_start: 0.7645 (mp0) cc_final: 0.7413 (mp0) REVERT: A 586 ASP cc_start: 0.7179 (m-30) cc_final: 0.6928 (m-30) REVERT: B 65 PHE cc_start: 0.8428 (m-10) cc_final: 0.8169 (m-10) REVERT: B 354 ASN cc_start: 0.7674 (t0) cc_final: 0.7393 (t0) REVERT: B 755 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: B 984 LEU cc_start: 0.8659 (tp) cc_final: 0.8284 (tp) REVERT: C 134 GLN cc_start: 0.7545 (tp40) cc_final: 0.6501 (mp10) REVERT: C 135 PHE cc_start: 0.6409 (m-10) cc_final: 0.6130 (m-10) REVERT: C 244 LEU cc_start: 0.7911 (mp) cc_final: 0.7700 (mp) REVERT: C 329 PHE cc_start: 0.7223 (m-10) cc_final: 0.6924 (m-80) REVERT: C 394 ASN cc_start: 0.8026 (p0) cc_final: 0.7747 (p0) REVERT: H 50 TYR cc_start: 0.5320 (m-10) cc_final: 0.5010 (m-80) REVERT: H 70 ILE cc_start: 0.6421 (tt) cc_final: 0.6125 (tp) REVERT: H 106 LEU cc_start: 0.5340 (tt) cc_final: 0.4840 (tt) REVERT: L 4 MET cc_start: 0.6559 (mmp) cc_final: 0.6343 (mmp) REVERT: M 99 ASP cc_start: 0.6752 (p0) cc_final: 0.6004 (p0) REVERT: M 149 LEU cc_start: 0.5129 (tp) cc_final: 0.4774 (tp) REVERT: N 118 PHE cc_start: 0.3834 (m-80) cc_final: 0.3139 (m-80) REVERT: O 60 TYR cc_start: 0.7797 (m-80) cc_final: 0.7380 (m-80) REVERT: O 65 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7440 (mmmm) REVERT: O 72 ARG cc_start: 0.4040 (ptp-110) cc_final: 0.3159 (ptm160) outliers start: 5 outliers final: 0 residues processed: 461 average time/residue: 0.4524 time to fit residues: 346.6464 Evaluate side-chains 283 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 755 GLN 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: 0.0470 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: 4.9990 chunk 395 optimal weight: 7.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1002 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 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** H 172 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 GLN O 179 GLN P 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 34394 Z= 0.313 Angle : 0.693 11.508 46854 Z= 0.365 Chirality : 0.047 0.210 5359 Planarity : 0.006 0.100 6046 Dihedral : 5.262 45.001 4670 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.08 % Favored : 93.71 % Rotamer: Outliers : 1.75 % Allowed : 7.82 % Favored : 90.44 % 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: -0.65 (0.13), residues: 4310 helix: 1.13 (0.20), residues: 703 sheet: -0.19 (0.15), residues: 1088 loop : -1.00 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 101 HIS 0.009 0.001 HIS B 66 PHE 0.028 0.002 PHE A 133 TYR 0.045 0.002 TYR L 49 ARG 0.010 0.001 ARG O 19 *********************** 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 386 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.6231 (pttt) cc_final: 0.5986 (pttt) REVERT: A 931 ILE cc_start: 0.8768 (mm) cc_final: 0.8523 (mt) REVERT: B 354 ASN cc_start: 0.7676 (t0) cc_final: 0.7399 (t0) REVERT: B 755 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: B 1125 ASN cc_start: 0.7377 (p0) cc_final: 0.7082 (p0) REVERT: C 191 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 244 LEU cc_start: 0.8108 (mp) cc_final: 0.7893 (mp) REVERT: C 377 PHE cc_start: 0.8330 (t80) cc_final: 0.8125 (t80) REVERT: C 997 ILE cc_start: 0.9438 (tp) cc_final: 0.9120 (tt) REVERT: H 38 ARG cc_start: 0.7358 (mtm180) cc_final: 0.6770 (mmt180) REVERT: H 101 TRP cc_start: 0.4848 (p-90) cc_final: 0.3907 (p-90) REVERT: H 106 LEU cc_start: 0.5257 (tt) cc_final: 0.4800 (tt) REVERT: L 126 LYS cc_start: 0.3216 (pttp) cc_final: 0.2935 (ptpp) REVERT: M 34 MET cc_start: 0.6775 (mmm) cc_final: 0.6218 (ttm) REVERT: M 98 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.5212 (ptp-170) REVERT: M 99 ASP cc_start: 0.7842 (p0) cc_final: 0.7075 (p0) REVERT: N 4 MET cc_start: 0.3189 (mtp) cc_final: 0.2621 (pmm) REVERT: N 118 PHE cc_start: 0.3461 (m-80) cc_final: 0.2974 (m-80) REVERT: P 149 LYS cc_start: 0.4718 (OUTLIER) cc_final: 0.4110 (mppt) outliers start: 65 outliers final: 43 residues processed: 363 average time/residue: 0.4537 time to fit residues: 274.7160 Evaluate side-chains 322 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain P residue 149 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 395 optimal weight: 7.9990 chunk 427 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 392 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 163 ASN H 172 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34394 Z= 0.304 Angle : 0.650 12.744 46854 Z= 0.340 Chirality : 0.046 0.206 5359 Planarity : 0.005 0.098 6046 Dihedral : 5.131 48.431 4670 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.45 % Favored : 93.36 % Rotamer: Outliers : 2.42 % Allowed : 11.07 % Favored : 86.52 % 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: -0.66 (0.13), residues: 4310 helix: 1.03 (0.20), residues: 712 sheet: -0.25 (0.15), residues: 1156 loop : -0.97 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 101 HIS 0.029 0.001 HIS B 245 PHE 0.026 0.002 PHE A 133 TYR 0.026 0.002 TYR P 32 ARG 0.005 0.001 ARG N 61 *********************** 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 405 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 315 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7380 (tm-30) cc_final: 0.6649 (tm-30) REVERT: A 224 GLU cc_start: 0.7842 (mp0) cc_final: 0.7502 (pm20) REVERT: A 558 LYS cc_start: 0.6382 (pttt) cc_final: 0.6064 (pttt) REVERT: A 931 ILE cc_start: 0.8809 (mm) cc_final: 0.8586 (mt) REVERT: B 338 PHE cc_start: 0.8113 (m-80) cc_final: 0.7899 (m-80) REVERT: B 354 ASN cc_start: 0.7745 (t0) cc_final: 0.7430 (t0) REVERT: B 423 TYR cc_start: 0.8115 (t80) cc_final: 0.7853 (t80) REVERT: B 755 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: B 1125 ASN cc_start: 0.7445 (p0) cc_final: 0.7160 (p0) REVERT: C 216 LEU cc_start: 0.7290 (mt) cc_final: 0.6350 (pp) REVERT: C 244 LEU cc_start: 0.8071 (mp) cc_final: 0.7785 (mp) REVERT: C 997 ILE cc_start: 0.9484 (tp) cc_final: 0.9161 (tt) REVERT: H 38 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6860 (mmt180) REVERT: H 60 TYR cc_start: 0.8071 (m-80) cc_final: 0.7716 (m-80) REVERT: H 101 TRP cc_start: 0.4685 (p-90) cc_final: 0.3627 (p-90) REVERT: H 106 LEU cc_start: 0.5469 (tt) cc_final: 0.5251 (tt) REVERT: L 4 MET cc_start: 0.5581 (mmp) cc_final: 0.5297 (mmp) REVERT: L 183 LYS cc_start: 0.3486 (tptt) cc_final: 0.2506 (pttt) REVERT: M 34 MET cc_start: 0.6821 (mmm) cc_final: 0.6189 (ttm) REVERT: M 98 ARG cc_start: 0.5727 (ttm-80) cc_final: 0.5445 (ptp-170) REVERT: M 99 ASP cc_start: 0.7772 (p0) cc_final: 0.6985 (p0) REVERT: N 118 PHE cc_start: 0.3603 (m-80) cc_final: 0.2938 (m-80) REVERT: N 147 GLN cc_start: 0.6259 (mt0) cc_final: 0.5675 (mt0) REVERT: O 60 TYR cc_start: 0.7625 (m-80) cc_final: 0.7232 (m-80) REVERT: O 100 ARG cc_start: 0.5629 (ptp90) cc_final: 0.4879 (ptp90) outliers start: 90 outliers final: 61 residues processed: 379 average time/residue: 0.4403 time to fit residues: 281.9674 Evaluate side-chains 333 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 271 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain P residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 20.0000 chunk 297 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 43 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 397 optimal weight: 4.9990 chunk 420 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 422 ASN B 992 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 172 HIS ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34394 Z= 0.281 Angle : 0.629 11.401 46854 Z= 0.329 Chirality : 0.046 0.191 5359 Planarity : 0.005 0.076 6046 Dihedral : 5.079 52.670 4670 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.55 % Rotamer: Outliers : 2.55 % Allowed : 13.38 % Favored : 84.07 % 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: -0.68 (0.13), residues: 4310 helix: 1.06 (0.20), residues: 712 sheet: -0.33 (0.15), residues: 1149 loop : -0.95 (0.13), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 105 HIS 0.008 0.001 HIS B 66 PHE 0.024 0.002 PHE H 68 TYR 0.022 0.002 TYR P 32 ARG 0.008 0.001 ARG H 100 *********************** 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 389 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 294 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4404 (mpp) cc_final: 0.4161 (mmm) REVERT: A 224 GLU cc_start: 0.7917 (mp0) cc_final: 0.7543 (pm20) REVERT: A 558 LYS cc_start: 0.6458 (pttt) cc_final: 0.6137 (pttt) REVERT: A 745 ASP cc_start: 0.6866 (p0) cc_final: 0.6643 (p0) REVERT: B 354 ASN cc_start: 0.7711 (t0) cc_final: 0.7403 (t0) REVERT: B 755 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: B 1125 ASN cc_start: 0.7465 (p0) cc_final: 0.7185 (p0) REVERT: C 997 ILE cc_start: 0.9498 (tp) cc_final: 0.9194 (tt) REVERT: H 60 TYR cc_start: 0.8123 (m-80) cc_final: 0.7764 (m-80) REVERT: H 101 TRP cc_start: 0.4737 (p-90) cc_final: 0.3701 (p-90) REVERT: H 116 LEU cc_start: 0.7101 (tp) cc_final: 0.6700 (pt) REVERT: L 183 LYS cc_start: 0.3501 (tptt) cc_final: 0.2430 (pttt) REVERT: M 34 MET cc_start: 0.6840 (mmm) cc_final: 0.6284 (ttm) REVERT: M 98 ARG cc_start: 0.5866 (ttm-80) cc_final: 0.5382 (ptp-170) REVERT: M 99 ASP cc_start: 0.7720 (p0) cc_final: 0.6998 (p0) REVERT: N 4 MET cc_start: 0.3470 (mtp) cc_final: 0.3145 (ptp) REVERT: N 147 GLN cc_start: 0.6348 (mt0) cc_final: 0.5818 (mp10) REVERT: O 60 TYR cc_start: 0.7719 (m-80) cc_final: 0.7403 (m-80) outliers start: 95 outliers final: 73 residues processed: 368 average time/residue: 0.4376 time to fit residues: 272.4263 Evaluate side-chains 332 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 258 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 313 optimal weight: 40.0000 chunk 173 optimal weight: 0.0370 chunk 358 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34394 Z= 0.194 Angle : 0.591 12.789 46854 Z= 0.306 Chirality : 0.044 0.203 5359 Planarity : 0.005 0.076 6046 Dihedral : 4.881 57.558 4670 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.57 % Favored : 94.24 % Rotamer: Outliers : 2.82 % Allowed : 14.34 % Favored : 82.84 % 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: -0.54 (0.13), residues: 4310 helix: 1.26 (0.20), residues: 706 sheet: -0.31 (0.15), residues: 1157 loop : -0.85 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 101 HIS 0.007 0.001 HIS B 66 PHE 0.025 0.002 PHE B 515 TYR 0.025 0.001 TYR L 186 ARG 0.004 0.000 ARG H 100 *********************** 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 405 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 300 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 224 GLU cc_start: 0.7941 (mp0) cc_final: 0.7508 (pm20) REVERT: A 558 LYS cc_start: 0.6459 (pttt) cc_final: 0.5858 (pttt) REVERT: B 68 ILE cc_start: 0.6527 (tp) cc_final: 0.5912 (tp) REVERT: B 354 ASN cc_start: 0.7728 (t0) cc_final: 0.7401 (t0) REVERT: B 755 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: B 1125 ASN cc_start: 0.7468 (p0) cc_final: 0.7212 (p0) REVERT: C 421 TYR cc_start: 0.4821 (OUTLIER) cc_final: 0.3044 (m-80) REVERT: C 896 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8591 (tp) REVERT: C 997 ILE cc_start: 0.9463 (tp) cc_final: 0.9128 (tt) REVERT: H 38 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6586 (mmt180) REVERT: H 60 TYR cc_start: 0.8100 (m-80) cc_final: 0.7650 (m-80) REVERT: H 101 TRP cc_start: 0.4727 (p-90) cc_final: 0.3234 (p-90) REVERT: H 116 LEU cc_start: 0.7134 (tp) cc_final: 0.6865 (pt) REVERT: H 190 VAL cc_start: 0.1536 (OUTLIER) cc_final: 0.1014 (p) REVERT: L 183 LYS cc_start: 0.3462 (tptt) cc_final: 0.2473 (pttt) REVERT: M 34 MET cc_start: 0.6928 (mmm) cc_final: 0.6509 (ttm) REVERT: M 98 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5504 (ptp-170) REVERT: M 99 ASP cc_start: 0.7664 (p0) cc_final: 0.7014 (p0) REVERT: N 4 MET cc_start: 0.3456 (mtp) cc_final: 0.3129 (ptp) REVERT: N 118 PHE cc_start: 0.3568 (m-80) cc_final: 0.2800 (m-80) REVERT: N 147 GLN cc_start: 0.6351 (mt0) cc_final: 0.5812 (mp10) REVERT: O 60 TYR cc_start: 0.7751 (m-80) cc_final: 0.7495 (m-80) outliers start: 105 outliers final: 69 residues processed: 382 average time/residue: 0.4246 time to fit residues: 274.3370 Evaluate side-chains 349 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 275 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain P residue 29 ILE 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: 5.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 420 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 949 GLN A1108 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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 39 GLN H 172 HIS H 205 ASN L 38 GLN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 34394 Z= 0.382 Angle : 0.672 11.355 46854 Z= 0.351 Chirality : 0.046 0.193 5359 Planarity : 0.005 0.078 6046 Dihedral : 5.169 53.483 4670 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.84 % Allowed : 14.26 % Favored : 81.90 % 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: -0.69 (0.13), residues: 4310 helix: 1.04 (0.20), residues: 713 sheet: -0.36 (0.14), residues: 1176 loop : -0.95 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP P 35 HIS 0.007 0.001 HIS A 69 PHE 0.023 0.002 PHE A 238 TYR 0.029 0.002 TYR L 173 ARG 0.010 0.001 ARG L 142 *********************** 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 413 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 270 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6949 (tm-30) REVERT: A 177 MET cc_start: 0.4095 (mpp) cc_final: 0.3840 (mmm) REVERT: A 335 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5981 (mt) REVERT: A 558 LYS cc_start: 0.6595 (pttt) cc_final: 0.5799 (pttt) REVERT: A 957 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 1092 GLU cc_start: 0.6465 (pm20) cc_final: 0.6039 (pm20) REVERT: B 338 PHE cc_start: 0.8025 (m-80) cc_final: 0.7601 (m-80) REVERT: B 354 ASN cc_start: 0.7912 (t0) cc_final: 0.7566 (t0) REVERT: B 755 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: B 1125 ASN cc_start: 0.7671 (p0) cc_final: 0.7416 (p0) REVERT: C 421 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.3257 (m-80) REVERT: C 896 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 997 ILE cc_start: 0.9517 (tp) cc_final: 0.9218 (tt) REVERT: H 38 ARG cc_start: 0.7291 (mtm110) cc_final: 0.6626 (mmt180) REVERT: H 60 TYR cc_start: 0.8080 (m-80) cc_final: 0.7662 (m-80) REVERT: H 116 LEU cc_start: 0.7341 (tp) cc_final: 0.7102 (pt) REVERT: H 190 VAL cc_start: 0.1001 (OUTLIER) cc_final: 0.0776 (p) REVERT: M 34 MET cc_start: 0.6906 (mmm) cc_final: 0.6156 (ttm) REVERT: M 98 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.5047 (ptp-170) REVERT: M 99 ASP cc_start: 0.7533 (p0) cc_final: 0.7016 (p0) REVERT: N 147 GLN cc_start: 0.6322 (mt0) cc_final: 0.5760 (mp10) REVERT: O 34 MET cc_start: 0.6023 (ttt) cc_final: 0.5790 (tmt) REVERT: O 60 TYR cc_start: 0.7873 (m-80) cc_final: 0.7667 (m-80) outliers start: 143 outliers final: 107 residues processed: 387 average time/residue: 0.4124 time to fit residues: 272.8006 Evaluate side-chains 361 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 248 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 354 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 419 optimal weight: 0.5980 chunk 262 optimal weight: 0.4980 chunk 255 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** 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 ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN P 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34394 Z= 0.233 Angle : 0.605 9.872 46854 Z= 0.315 Chirality : 0.045 0.193 5359 Planarity : 0.005 0.077 6046 Dihedral : 4.937 43.897 4670 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 2.90 % Allowed : 15.71 % Favored : 81.39 % 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: -0.59 (0.13), residues: 4310 helix: 1.20 (0.20), residues: 714 sheet: -0.40 (0.15), residues: 1153 loop : -0.85 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 35 HIS 0.006 0.001 HIS A 69 PHE 0.026 0.002 PHE P 73 TYR 0.024 0.001 TYR B 265 ARG 0.017 0.001 ARG A 214 *********************** 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 395 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 287 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6611 (m-10) cc_final: 0.6284 (m-10) REVERT: A 173 GLN cc_start: 0.7586 (tm-30) cc_final: 0.6999 (tm-30) REVERT: A 558 LYS cc_start: 0.6667 (pttt) cc_final: 0.5885 (pttt) REVERT: A 957 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 1032 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7377 (m) REVERT: A 1092 GLU cc_start: 0.6377 (pm20) cc_final: 0.6034 (pm20) REVERT: B 18 LEU cc_start: 0.4770 (mp) cc_final: 0.4453 (mp) REVERT: B 338 PHE cc_start: 0.7993 (m-80) cc_final: 0.7630 (m-80) REVERT: B 354 ASN cc_start: 0.7836 (t0) cc_final: 0.7514 (t0) REVERT: B 988 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 1125 ASN cc_start: 0.7606 (p0) cc_final: 0.7359 (p0) REVERT: C 421 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.3254 (m-80) REVERT: C 896 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8744 (tp) REVERT: C 997 ILE cc_start: 0.9474 (tp) cc_final: 0.9165 (tt) REVERT: H 60 TYR cc_start: 0.8060 (m-80) cc_final: 0.7600 (m-80) REVERT: H 116 LEU cc_start: 0.7495 (tp) cc_final: 0.7244 (pt) REVERT: H 190 VAL cc_start: 0.1062 (OUTLIER) cc_final: 0.0838 (p) REVERT: L 4 MET cc_start: 0.5535 (mmp) cc_final: 0.5274 (mmp) REVERT: M 34 MET cc_start: 0.6896 (mmm) cc_final: 0.5749 (ttm) REVERT: M 98 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.4704 (ptp-170) REVERT: M 99 ASP cc_start: 0.7559 (p0) cc_final: 0.6971 (p0) REVERT: N 4 MET cc_start: 0.3749 (mtp) cc_final: 0.3398 (ptp) REVERT: N 147 GLN cc_start: 0.6353 (mt0) cc_final: 0.5785 (mp10) REVERT: O 34 MET cc_start: 0.6132 (ttt) cc_final: 0.5829 (tmt) REVERT: O 60 TYR cc_start: 0.7811 (m-80) cc_final: 0.7551 (m-80) REVERT: O 100 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5415 (ptp90) outliers start: 108 outliers final: 89 residues processed: 367 average time/residue: 0.4219 time to fit residues: 264.4058 Evaluate side-chains 357 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 262 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34394 Z= 0.252 Angle : 0.609 9.765 46854 Z= 0.317 Chirality : 0.045 0.347 5359 Planarity : 0.005 0.079 6046 Dihedral : 4.857 36.445 4667 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.94 % Favored : 93.92 % Rotamer: Outliers : 3.28 % Allowed : 15.71 % Favored : 81.01 % 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: -0.59 (0.13), residues: 4310 helix: 1.18 (0.20), residues: 719 sheet: -0.40 (0.14), residues: 1195 loop : -0.85 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 105 HIS 0.005 0.001 HIS A 69 PHE 0.024 0.002 PHE B 194 TYR 0.021 0.001 TYR H 153 ARG 0.008 0.000 ARG A 765 *********************** 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 403 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 281 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6681 (m-10) cc_final: 0.6328 (m-10) REVERT: A 173 GLN cc_start: 0.7551 (tm-30) cc_final: 0.6989 (tm-30) REVERT: A 558 LYS cc_start: 0.6686 (pttt) cc_final: 0.6013 (pttt) REVERT: A 957 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 1032 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7425 (m) REVERT: A 1092 GLU cc_start: 0.6395 (pm20) cc_final: 0.6043 (pm20) REVERT: B 18 LEU cc_start: 0.4771 (mp) cc_final: 0.4458 (mp) REVERT: B 338 PHE cc_start: 0.7987 (m-80) cc_final: 0.7667 (m-80) REVERT: B 351 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8604 (p90) REVERT: B 354 ASN cc_start: 0.7855 (t0) cc_final: 0.7530 (t0) REVERT: B 1125 ASN cc_start: 0.7583 (p0) cc_final: 0.7338 (p0) REVERT: C 421 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.3259 (m-80) REVERT: C 856 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8518 (p0) REVERT: C 896 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8706 (tp) REVERT: C 997 ILE cc_start: 0.9484 (tp) cc_final: 0.9170 (tt) REVERT: H 38 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6602 (mmt180) REVERT: H 60 TYR cc_start: 0.8067 (m-80) cc_final: 0.7561 (m-80) REVERT: H 116 LEU cc_start: 0.7623 (tp) cc_final: 0.7371 (pt) REVERT: H 190 VAL cc_start: 0.1066 (OUTLIER) cc_final: 0.0830 (p) REVERT: L 4 MET cc_start: 0.5305 (mmp) cc_final: 0.5060 (mmp) REVERT: L 183 LYS cc_start: 0.3363 (tptt) cc_final: 0.2341 (pttt) REVERT: M 34 MET cc_start: 0.6618 (mmm) cc_final: 0.6047 (ttm) REVERT: M 98 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.4598 (ptp-170) REVERT: M 99 ASP cc_start: 0.7512 (p0) cc_final: 0.7010 (p0) REVERT: N 147 GLN cc_start: 0.6318 (mt0) cc_final: 0.5757 (mp10) REVERT: O 34 MET cc_start: 0.6193 (ttt) cc_final: 0.5881 (tmt) REVERT: O 100 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5497 (ptp90) outliers start: 122 outliers final: 101 residues processed: 375 average time/residue: 0.4461 time to fit residues: 284.3262 Evaluate side-chains 371 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 262 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 366 optimal weight: 0.9980 chunk 390 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 353 optimal weight: 8.9990 chunk 369 optimal weight: 6.9990 chunk 389 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 196 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 777 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34394 Z= 0.211 Angle : 0.594 9.727 46854 Z= 0.309 Chirality : 0.044 0.253 5359 Planarity : 0.005 0.077 6046 Dihedral : 4.731 34.522 4667 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 3.01 % Allowed : 16.28 % Favored : 80.71 % 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: -0.54 (0.13), residues: 4310 helix: 1.23 (0.20), residues: 720 sheet: -0.37 (0.14), residues: 1192 loop : -0.82 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M 105 HIS 0.004 0.001 HIS B 207 PHE 0.028 0.002 PHE B 65 TYR 0.026 0.001 TYR H 153 ARG 0.010 0.000 ARG A 765 *********************** 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 391 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 279 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6532 (m-10) cc_final: 0.6240 (m-10) REVERT: A 173 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7063 (tm-30) REVERT: A 335 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6086 (mt) REVERT: A 558 LYS cc_start: 0.6680 (pttt) cc_final: 0.5994 (pttt) REVERT: A 957 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 1032 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7389 (m) REVERT: A 1092 GLU cc_start: 0.6406 (pm20) cc_final: 0.6071 (pm20) REVERT: B 18 LEU cc_start: 0.4741 (mp) cc_final: 0.4435 (mp) REVERT: B 78 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5907 (mtm-85) REVERT: B 312 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8817 (tt) REVERT: B 338 PHE cc_start: 0.7987 (m-80) cc_final: 0.7669 (m-80) REVERT: B 351 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8602 (p90) REVERT: B 354 ASN cc_start: 0.7817 (t0) cc_final: 0.7463 (t0) REVERT: B 1125 ASN cc_start: 0.7602 (p0) cc_final: 0.7348 (p0) REVERT: C 421 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.3208 (m-80) REVERT: C 896 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8712 (tp) REVERT: C 997 ILE cc_start: 0.9469 (tp) cc_final: 0.9161 (tt) REVERT: H 60 TYR cc_start: 0.8040 (m-80) cc_final: 0.7497 (m-80) REVERT: H 116 LEU cc_start: 0.7797 (tp) cc_final: 0.7498 (pt) REVERT: H 190 VAL cc_start: 0.1002 (OUTLIER) cc_final: 0.0775 (p) REVERT: L 4 MET cc_start: 0.5403 (mmp) cc_final: 0.5135 (mmp) REVERT: L 118 PHE cc_start: 0.1978 (m-10) cc_final: 0.1584 (m-80) REVERT: M 34 MET cc_start: 0.6581 (mmm) cc_final: 0.5819 (ttt) REVERT: M 98 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.4472 (ptp-170) REVERT: M 99 ASP cc_start: 0.7582 (p0) cc_final: 0.7105 (p0) REVERT: N 147 GLN cc_start: 0.6376 (mt0) cc_final: 0.5839 (mp10) REVERT: O 100 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5576 (ptp90) outliers start: 112 outliers final: 94 residues processed: 362 average time/residue: 0.4220 time to fit residues: 258.0751 Evaluate side-chains 369 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 265 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL 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: 1.9990 chunk 252 optimal weight: 0.2980 chunk 195 optimal weight: 0.9980 chunk 287 optimal weight: 0.7980 chunk 433 optimal weight: 8.9990 chunk 398 optimal weight: 40.0000 chunk 345 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34394 Z= 0.199 Angle : 0.588 9.658 46854 Z= 0.306 Chirality : 0.044 0.190 5359 Planarity : 0.005 0.077 6046 Dihedral : 4.652 33.396 4667 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 3.14 % Allowed : 16.20 % Favored : 80.66 % 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: -0.50 (0.13), residues: 4310 helix: 1.28 (0.20), residues: 725 sheet: -0.31 (0.15), residues: 1178 loop : -0.83 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP M 105 HIS 0.004 0.001 HIS B 207 PHE 0.031 0.001 PHE B 65 TYR 0.027 0.001 TYR H 153 ARG 0.010 0.000 ARG A 765 ********************** 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 403 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 286 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7055 (tm-30) REVERT: A 335 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6080 (mt) REVERT: A 558 LYS cc_start: 0.6677 (pttt) cc_final: 0.5992 (pttt) REVERT: A 957 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 1032 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7348 (m) REVERT: A 1092 GLU cc_start: 0.6384 (pm20) cc_final: 0.6055 (pm20) REVERT: B 18 LEU cc_start: 0.4780 (mp) cc_final: 0.4492 (mp) REVERT: B 78 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5856 (mtm-85) REVERT: B 312 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8797 (tt) REVERT: B 338 PHE cc_start: 0.7966 (m-80) cc_final: 0.7654 (m-80) REVERT: B 351 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8576 (p90) REVERT: B 354 ASN cc_start: 0.7822 (t0) cc_final: 0.7483 (t0) REVERT: B 1125 ASN cc_start: 0.7610 (p0) cc_final: 0.7373 (p0) REVERT: C 421 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.3295 (m-80) REVERT: C 856 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8473 (p0) REVERT: C 896 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8703 (tp) REVERT: C 997 ILE cc_start: 0.9461 (tp) cc_final: 0.9153 (tt) REVERT: H 38 ARG cc_start: 0.7222 (mtm180) cc_final: 0.6608 (mmt180) REVERT: H 60 TYR cc_start: 0.8027 (m-80) cc_final: 0.7459 (m-80) REVERT: H 116 LEU cc_start: 0.7806 (tp) cc_final: 0.7512 (pt) REVERT: H 190 VAL cc_start: 0.1030 (OUTLIER) cc_final: 0.0798 (p) REVERT: L 4 MET cc_start: 0.5384 (mmp) cc_final: 0.5147 (mmp) REVERT: L 118 PHE cc_start: 0.1961 (m-10) cc_final: 0.1578 (m-80) REVERT: M 34 MET cc_start: 0.6693 (mmm) cc_final: 0.5901 (ttt) REVERT: N 147 GLN cc_start: 0.6370 (mt0) cc_final: 0.5804 (mp10) REVERT: O 100 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5592 (ptp90) outliers start: 117 outliers final: 97 residues processed: 370 average time/residue: 0.4546 time to fit residues: 288.0500 Evaluate side-chains 375 residues out of total 3815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 268 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 100 ARG Chi-restraints excluded: chain O residue 101 TRP Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 0.9990 chunk 367 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 144 optimal weight: 0.0970 chunk 354 optimal weight: 0.0030 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 580 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.143854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100874 restraints weight = 93958.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102713 restraints weight = 60207.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103502 restraints weight = 32175.680| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34394 Z= 0.238 Angle : 0.600 9.657 46854 Z= 0.313 Chirality : 0.045 0.190 5359 Planarity : 0.005 0.077 6046 Dihedral : 4.676 32.512 4667 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 3.22 % Allowed : 16.22 % Favored : 80.55 % 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: -0.50 (0.13), residues: 4310 helix: 1.36 (0.20), residues: 708 sheet: -0.34 (0.15), residues: 1162 loop : -0.82 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 105 HIS 0.004 0.001 HIS B 69 PHE 0.033 0.002 PHE B 65 TYR 0.025 0.001 TYR H 153 ARG 0.008 0.000 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7097.38 seconds wall clock time: 130 minutes 47.95 seconds (7847.95 seconds total)