Starting phenix.real_space_refine on Fri Dec 15 06:35:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/12_2023/7uz7_26881.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 132 5.16 5 C 19419 2.51 5 N 5019 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 68": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30552 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.10, per 1000 atoms: 0.53 Number of scatterers: 30552 At special positions: 0 Unit cell: (164.736, 161.408, 188.032, 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 132 16.00 O 5982 8.00 N 5019 7.00 C 19419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 11.12 Conformation dependent library (CDL) restraints added in 5.6 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 60 sheets defined 19.9% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.725A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.069A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.813A 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 816 through 826 removed outlier: 3.667A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.579A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 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: 3.596A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.730A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.664A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 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 984 removed outlier: 3.625A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.794A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.548A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.720A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.065A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.809A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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: 3.619A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.679A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.754A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.789A pdb=" N ASN M 36 " --> pdb=" O ASN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.742A pdb=" N ASN P 36 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.894A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.792A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.194A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 435 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.682A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.647A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.642A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.906A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.615A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.948A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.692A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.723A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.100A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.638A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.187A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.720A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.517A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.111A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.637A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.735A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.970A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 66 through 67 removed outlier: 5.082A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.031A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.169A pdb=" N GLU L 125 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.975A pdb=" N GLN M 3 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 66 through 67 removed outlier: 5.087A pdb=" N TRP M 52 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS M 43 " --> pdb=" O TRP M 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 54 " --> pdb=" O TRP M 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.801A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.670A pdb=" N GLU N 125 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR N 122 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.984A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL P 19 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 66 through 67 removed outlier: 5.048A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 122 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.846A pdb=" N THR Q 5 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS Q 23 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE Q 87 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE Q 54 " --> pdb=" O TRP Q 41 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN Q 43 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU Q 52 " --> pdb=" O GLN Q 43 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3174 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: 17.32 Time building geometry restraints manager: 12.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 4372 1.25 - 1.39: 8349 1.39 - 1.54: 17592 1.54 - 1.68: 773 1.68 - 1.82: 171 Bond restraints: 31257 Sorted by residual: bond pdb=" CG PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.503 1.100 0.403 3.40e-02 8.65e+02 1.40e+02 bond pdb=" CG PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N ASN C 801 " pdb=" CA ASN C 801 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.98e+00 ... (remaining 31252 not shown) Histogram of bond angle deviations from ideal: 80.75 - 91.41: 4 91.41 - 102.06: 50 102.06 - 112.72: 17377 112.72 - 123.38: 24280 123.38 - 134.04: 871 Bond angle restraints: 42582 Sorted by residual: angle pdb=" N PRO A1079 " pdb=" CD PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 103.20 80.75 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" N PRO B1079 " pdb=" CD PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 97.65 14.35 1.40e+00 5.10e-01 1.05e+02 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 98.42 13.58 1.40e+00 5.10e-01 9.41e+01 angle pdb=" CA PRO A1079 " pdb=" CB PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 104.50 89.34 15.16 1.90e+00 2.77e-01 6.37e+01 ... (remaining 42577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 17978 21.67 - 43.35: 968 43.35 - 65.02: 139 65.02 - 86.69: 47 86.69 - 108.36: 11 Dihedral angle restraints: 19143 sinusoidal: 7920 harmonic: 11223 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 167.97 -74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 104 " pdb=" CB CYS N 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.23 -70.23 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 104 " pdb=" CB CYS Q 104 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4130 0.058 - 0.115: 747 0.115 - 0.173: 63 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 4941 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.228 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG A1307 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.226 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG B1307 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " -0.222 2.00e-02 2.50e+03 1.89e-01 4.49e+02 pdb=" C7 NAG C1307 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.008 2.00e-02 2.50e+03 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 521 2.68 - 3.23: 29270 3.23 - 3.79: 47533 3.79 - 4.34: 65317 4.34 - 4.90: 107380 Nonbonded interactions: 250021 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.121 2.440 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.195 2.440 nonbonded pdb=" OE1 GLN B 804 " pdb=" NE2 GLN B 935 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.209 2.440 ... (remaining 250016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.030 Extract box with map and model: 11.230 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 85.100 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 0.403 31257 Z= 0.277 Angle : 0.607 22.452 42582 Z= 0.327 Chirality : 0.044 0.289 4944 Planarity : 0.006 0.195 5457 Dihedral : 13.463 108.363 11811 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3813 helix: 1.79 (0.21), residues: 672 sheet: 0.32 (0.17), residues: 888 loop : -0.64 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.002 0.001 HIS B 655 PHE 0.023 0.001 PHE A 906 TYR 0.025 0.001 TYR B 248 ARG 0.005 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 1.2314 time to fit residues: 369.0877 Evaluate side-chains 151 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.9467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.0040 chunk 288 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 345 optimal weight: 50.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 913 GLN A1010 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31257 Z= 0.336 Angle : 0.623 11.122 42582 Z= 0.316 Chirality : 0.047 0.316 4944 Planarity : 0.004 0.051 5457 Dihedral : 7.807 77.147 5082 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.85 % Allowed : 8.93 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.06 (0.13), residues: 3813 helix: 1.52 (0.21), residues: 660 sheet: 0.41 (0.18), residues: 867 loop : -0.69 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.006 0.001 HIS C1088 PHE 0.027 0.002 PHE C1121 TYR 0.033 0.002 TYR B 265 ARG 0.008 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 189 average time/residue: 1.0703 time to fit residues: 254.4939 Evaluate side-chains 155 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 4.4413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 346 optimal weight: 8.9990 chunk 374 optimal weight: 40.0000 chunk 308 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 913 GLN A 955 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 207 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31257 Z= 0.238 Angle : 0.564 11.083 42582 Z= 0.285 Chirality : 0.045 0.317 4944 Planarity : 0.004 0.039 5457 Dihedral : 6.838 59.996 5082 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 11.23 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.03 (0.13), residues: 3813 helix: 1.75 (0.21), residues: 654 sheet: 0.55 (0.18), residues: 822 loop : -0.69 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.004 0.001 HIS C1088 PHE 0.019 0.001 PHE C1121 TYR 0.027 0.001 TYR B 265 ARG 0.006 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 157 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 199 average time/residue: 1.0984 time to fit residues: 275.8623 Evaluate side-chains 170 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 2 average time/residue: 1.8636 time to fit residues: 8.7230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 40.0000 chunk 260 optimal weight: 7.9990 chunk 179 optimal weight: 0.0870 chunk 38 optimal weight: 0.0570 chunk 165 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 chunk 347 optimal weight: 50.0000 chunk 368 optimal weight: 50.0000 chunk 181 optimal weight: 0.6980 chunk 329 optimal weight: 40.0000 chunk 99 optimal weight: 0.9980 overall best weight: 1.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31257 Z= 0.239 Angle : 0.561 11.346 42582 Z= 0.283 Chirality : 0.045 0.319 4944 Planarity : 0.004 0.039 5457 Dihedral : 6.362 58.943 5082 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.03 % Allowed : 13.11 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.01 (0.13), residues: 3813 helix: 1.74 (0.21), residues: 660 sheet: 0.50 (0.17), residues: 849 loop : -0.72 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.020 0.001 PHE C 106 TYR 0.025 0.001 TYR C 170 ARG 0.009 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 154 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 41 residues processed: 214 average time/residue: 1.0765 time to fit residues: 290.4461 Evaluate side-chains 184 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 3.239 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 39 residues processed: 3 average time/residue: 0.8705 time to fit residues: 7.9359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 151 optimal weight: 0.0980 chunk 314 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 330 optimal weight: 50.0000 chunk 92 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31257 Z= 0.178 Angle : 0.532 11.156 42582 Z= 0.268 Chirality : 0.044 0.316 4944 Planarity : 0.003 0.039 5457 Dihedral : 5.961 59.524 5082 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.09 % Allowed : 14.11 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.12 (0.13), residues: 3813 helix: 1.94 (0.21), residues: 660 sheet: 0.59 (0.17), residues: 849 loop : -0.69 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.002 0.000 HIS C1088 PHE 0.016 0.001 PHE A1121 TYR 0.027 0.001 TYR C 170 ARG 0.002 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 150 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 45 residues processed: 209 average time/residue: 1.0453 time to fit residues: 277.0445 Evaluate side-chains 187 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 42 residues processed: 3 average time/residue: 0.7406 time to fit residues: 7.5556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 5.9990 chunk 331 optimal weight: 40.0000 chunk 72 optimal weight: 0.0070 chunk 216 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 368 optimal weight: 50.0000 chunk 306 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 787 GLN A1011 GLN A1106 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31257 Z= 0.291 Angle : 0.568 10.051 42582 Z= 0.287 Chirality : 0.045 0.321 4944 Planarity : 0.004 0.040 5457 Dihedral : 5.879 59.193 5082 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.51 % Allowed : 14.26 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.00 (0.13), residues: 3813 helix: 1.75 (0.20), residues: 660 sheet: 0.39 (0.17), residues: 900 loop : -0.70 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 PHE 0.025 0.002 PHE B1121 TYR 0.021 0.001 TYR A 170 ARG 0.009 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 149 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 47 residues processed: 224 average time/residue: 1.0736 time to fit residues: 306.3252 Evaluate side-chains 189 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 3.253 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 46 residues processed: 2 average time/residue: 0.3161 time to fit residues: 5.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 40.0000 chunk 41 optimal weight: 50.0000 chunk 210 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 367 optimal weight: 50.0000 chunk 229 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31257 Z= 0.227 Angle : 0.552 11.238 42582 Z= 0.278 Chirality : 0.045 0.319 4944 Planarity : 0.004 0.041 5457 Dihedral : 5.737 59.808 5082 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 2.27 % Allowed : 15.23 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3813 helix: 1.82 (0.20), residues: 660 sheet: 0.32 (0.16), residues: 936 loop : -0.69 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.022 0.001 PHE B1121 TYR 0.025 0.001 TYR C 170 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 153 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 48 residues processed: 221 average time/residue: 1.0423 time to fit residues: 293.0712 Evaluate side-chains 188 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 140 time to evaluate : 3.066 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 45 residues processed: 4 average time/residue: 0.5198 time to fit residues: 7.2177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 250 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 34 optimal weight: 0.0010 chunk 288 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31257 Z= 0.285 Angle : 0.580 12.498 42582 Z= 0.291 Chirality : 0.045 0.327 4944 Planarity : 0.004 0.043 5457 Dihedral : 5.760 59.517 5082 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.03 % Allowed : 15.74 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3813 helix: 1.71 (0.20), residues: 660 sheet: 0.25 (0.16), residues: 936 loop : -0.66 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 PHE 0.026 0.002 PHE B1121 TYR 0.021 0.001 TYR A 170 ARG 0.013 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 144 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 51 residues processed: 204 average time/residue: 1.0460 time to fit residues: 271.2239 Evaluate side-chains 190 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 3.315 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 47 residues processed: 5 average time/residue: 1.2411 time to fit residues: 12.5088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 5.9990 chunk 351 optimal weight: 30.0000 chunk 320 optimal weight: 0.0270 chunk 342 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 309 optimal weight: 0.6980 chunk 323 optimal weight: 9.9990 chunk 341 optimal weight: 20.0000 overall best weight: 3.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN M 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 31257 Z= 0.477 Angle : 0.660 13.181 42582 Z= 0.334 Chirality : 0.049 0.344 4944 Planarity : 0.004 0.043 5457 Dihedral : 6.073 58.205 5082 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 2.03 % Allowed : 15.99 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.34 (0.13), residues: 3813 helix: 1.25 (0.20), residues: 660 sheet: 0.07 (0.16), residues: 948 loop : -0.81 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.007 0.001 HIS C1088 PHE 0.038 0.002 PHE B1121 TYR 0.030 0.002 TYR B1067 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 146 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 50 residues processed: 207 average time/residue: 0.9872 time to fit residues: 260.8932 Evaluate side-chains 188 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 2.474 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 48 residues processed: 3 average time/residue: 0.2453 time to fit residues: 5.1803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 3.9990 chunk 361 optimal weight: 30.0000 chunk 220 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 349 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31257 Z= 0.191 Angle : 0.567 13.167 42582 Z= 0.284 Chirality : 0.045 0.331 4944 Planarity : 0.003 0.040 5457 Dihedral : 5.706 56.642 5082 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 1.70 % Allowed : 16.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.12 (0.13), residues: 3813 helix: 1.69 (0.20), residues: 660 sheet: 0.12 (0.16), residues: 966 loop : -0.72 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.002 0.000 HIS B1088 PHE 0.017 0.001 PHE A1121 TYR 0.025 0.001 TYR A 170 ARG 0.018 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 45 residues processed: 195 average time/residue: 0.9646 time to fit residues: 239.1387 Evaluate side-chains 176 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 2.488 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 45 residues processed: 0 time to fit residues: 3.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 6.9990 chunk 321 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 278 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 55 optimal weight: 7.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.221829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.151349 restraints weight = 42772.712| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.70 r_work: 0.3329 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31257 Z= 0.175 Angle : 0.558 13.302 42582 Z= 0.277 Chirality : 0.045 0.336 4944 Planarity : 0.003 0.042 5457 Dihedral : 5.504 55.430 5082 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 16.68 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.00 (0.13), residues: 3813 helix: 1.84 (0.20), residues: 660 sheet: 0.36 (0.17), residues: 912 loop : -0.72 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS C 207 PHE 0.017 0.001 PHE A1121 TYR 0.024 0.001 TYR B 170 ARG 0.006 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7314.20 seconds wall clock time: 160 minutes 38.22 seconds (9638.22 seconds total)