Starting phenix.real_space_refine on Sat Aug 10 01:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y8g_39045/08_2024/8y8g_39045.cif" } resolution = 3.23 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= 0.066 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 162 5.16 5 C 17737 2.51 5 N 4508 2.21 5 O 5421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27828 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 9108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9108 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 4 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 9073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9073 Classifications: {'peptide': 1170} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1113} 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: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 9216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9216 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.00, per 1000 atoms: 0.54 Number of scatterers: 27828 At special positions: 0 Unit cell: (147.6, 153.34, 209.92, 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 162 16.00 O 5421 8.00 N 4508 7.00 C 17737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 335 " " NAG A1304 " - " ASN A 664 " " NAG A1305 " - " ASN A 793 " " NAG A1306 " - " ASN A 355 " " NAG A1307 " - " ASN A1211 " " NAG A1308 " - " ASN A 58 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B 664 " " NAG B1303 " - " ASN B 725 " " NAG B1304 " - " ASN B 793 " " NAG C1301 " - " ASN C 192 " " NAG C1302 " - " ASN C 664 " " NAG C1303 " - " ASN C 703 " " NAG C1304 " - " ASN C 725 " " NAG C1305 " - " ASN C 793 " " NAG C1306 " - " ASN C 355 " " NAG C1307 " - " ASN C1211 " " NAG C1308 " - " ASN C 19 " " NAG D 1 " - " ASN C 188 " " NAG E 1 " - " ASN C 335 " " NAG F 1 " - " ASN C 132 " " NAG G 1 " - " ASN A 725 " " NAG H 1 " - " ASN B 132 " Time building additional restraints: 10.13 Conformation dependent library (CDL) restraints added in 4.5 seconds 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6646 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 59 sheets defined 23.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.687A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.626A pdb=" N GLU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.794A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.773A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 3.932A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.882A pdb=" N PHE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 4.000A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 861 removed outlier: 3.608A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 854 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.891A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 924 Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 991 removed outlier: 4.236A pdb=" N GLN C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 991 " --> pdb=" O ILE C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.771A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1019 removed outlier: 3.519A pdb=" N ASN C1009 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.954A pdb=" N LYS C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.529A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1066 through 1113 removed outlier: 5.096A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.511A pdb=" N TRP A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.509A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.666A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.692A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.880A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.614A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.660A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.562A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 4.003A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.502A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.819A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.871A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.655A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 removed outlier: 3.724A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.803A pdb=" N ASN A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.600A pdb=" N GLN A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.548A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.518A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1099 " --> pdb=" O ASP A1095 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.615A pdb=" N GLY B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.953A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.624A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.598A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 4.139A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.591A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.764A pdb=" N PHE B 817 " --> pdb=" O ASP B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.706A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 829 " --> pdb=" O CYS B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 836 removed outlier: 3.657A pdb=" N CYS B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 836' Processing helix chain 'B' and resid 837 through 862 removed outlier: 3.513A pdb=" N LEU B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.116A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.602A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.514A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 4.213A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 removed outlier: 3.604A pdb=" N GLN B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.841A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 999 " --> pdb=" O ASP B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1019 removed outlier: 3.593A pdb=" N ILE B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.529A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.719A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 3.625A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 3.775A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1099 " --> pdb=" O ASP B1095 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 60 through 67 removed outlier: 6.584A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.773A pdb=" N TYR C 199 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 211 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.052A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.509A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 190 removed outlier: 3.874A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 125 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 302 through 310 removed outlier: 4.467A pdb=" N VAL C 677 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY C 308 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 675 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG C 676 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG C 693 " --> pdb=" O ARG C 676 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 316 through 319 removed outlier: 7.514A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 667 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 658 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AA9, first strand: chain 'C' and resid 345 through 349 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 345 through 349 current: chain 'C' and resid 585 through 595 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.687A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.742A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.859A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 573 " --> pdb=" O GLY C 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 724 through 725 removed outlier: 6.744A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.019A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 786 through 791 removed outlier: 4.022A pdb=" N ILE C 788 " --> pdb=" O VAL C1156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1156 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 794 through 803 removed outlier: 3.646A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.298A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 866 through 868 removed outlier: 6.589A pdb=" N LEU C 867 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1202 through 1204 removed outlier: 3.693A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.508A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 60 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 68 current: chain 'A' and resid 197 through 204 removed outlier: 3.508A pdb=" N TYR A 199 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.944A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 109 through 113 removed outlier: 4.102A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AC7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.536A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.942A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.734A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 345 through 349 removed outlier: 4.089A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 367 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.721A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.553A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.694A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 573 " --> pdb=" O GLY A 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.736A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 786 through 789 Processing sheet with id=AD7, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.519A pdb=" N ALA A1137 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.270A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.681A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.863A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 1170 through 1172 removed outlier: 3.527A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1175 through 1180 Processing sheet with id=AE4, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.930A pdb=" N ASN B 26 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 60 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 61 current: chain 'B' and resid 197 through 205 removed outlier: 3.727A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 227 current: chain 'B' and resid 280 through 281 Processing sheet with id=AE6, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.810A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.664A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 189 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 109 through 113 removed outlier: 3.805A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 113 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AF1, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.708A pdb=" N GLY B 629 " --> pdb=" O TYR B 622 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF3, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.661A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 422 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AF5, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AF6, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.567A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AF8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AF9, first strand: chain 'B' and resid 724 through 725 removed outlier: 6.668A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 786 through 791 removed outlier: 3.605A pdb=" N ILE B 788 " --> pdb=" O VAL B1156 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B1156 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 794 through 803 removed outlier: 3.538A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.352A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.713A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1169 through 1172 removed outlier: 3.843A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2181 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: 11.48 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8822 1.34 - 1.46: 7077 1.46 - 1.58: 12411 1.58 - 1.70: 0 1.70 - 1.81: 188 Bond restraints: 28498 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 28493 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 811 107.14 - 113.85: 15786 113.85 - 120.55: 10673 120.55 - 127.26: 11321 127.26 - 133.97: 240 Bond angle restraints: 38831 Sorted by residual: angle pdb=" N VAL A 700 " pdb=" CA VAL A 700 " pdb=" C VAL A 700 " ideal model delta sigma weight residual 113.07 109.14 3.93 1.37e+00 5.33e-01 8.25e+00 angle pdb=" C PHE A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" N ASN B 664 " pdb=" CA ASN B 664 " pdb=" C ASN B 664 " ideal model delta sigma weight residual 108.63 112.31 -3.68 1.60e+00 3.91e-01 5.30e+00 angle pdb=" N TYR B 667 " pdb=" CA TYR B 667 " pdb=" C TYR B 667 " ideal model delta sigma weight residual 108.34 111.09 -2.75 1.31e+00 5.83e-01 4.41e+00 angle pdb=" C PHE B 130 " pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta sigma weight residual 121.97 118.21 3.76 1.80e+00 3.09e-01 4.36e+00 ... (remaining 38826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 17003 21.78 - 43.57: 327 43.57 - 65.35: 37 65.35 - 87.14: 7 87.14 - 108.92: 4 Dihedral angle restraints: 17378 sinusoidal: 7034 harmonic: 10344 Sorted by residual: dihedral pdb=" CB CYS B 925 " pdb=" SG CYS B 925 " pdb=" SG CYS B 936 " pdb=" CB CYS B 936 " ideal model delta sinusoidal sigma weight residual 93.00 134.79 -41.79 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA PHE A 98 " pdb=" C PHE A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.79 108.92 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3806 0.055 - 0.109: 590 0.109 - 0.164: 74 0.164 - 0.218: 0 0.218 - 0.273: 1 Chirality restraints: 4471 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1211 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 703 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 4468 not shown) Planarity restraints: 4994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A1067 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B1067 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 521 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 522 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " 0.023 5.00e-02 4.00e+02 ... (remaining 4991 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4650 2.77 - 3.30: 25483 3.30 - 3.83: 43500 3.83 - 4.37: 50159 4.37 - 4.90: 88280 Nonbonded interactions: 212072 Sorted by model distance: nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.236 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 266 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.242 3.040 nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.258 3.040 ... (remaining 212067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 163 or (resid 164 and (name N o \ r name CA or name C or name O or name CB )) or resid 165 or (resid 166 and (name \ N or name CA or name C or name O or name CB )) or resid 167 through 244 or resi \ d 254 through 363 or (resid 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 412 or (resid 413 and (name N or n \ ame CA or name C or name O or name CB )) or resid 414 through 446 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 45 \ 4 or (resid 455 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 491 or (resid 492 through 493 and (name N or name CA or name C or \ name O or name CB )) or resid 494 through 553 or (resid 554 and (name N or name \ CA or name C or name O or name CB )) or resid 555 through 557 or resid 563 throu \ gh 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 through 1065 or (resid 1066 and (name N or name CA or name C or name \ O or name CB )) or resid 1067 through 1221 or resid 1301 through 1304)) selection = (chain 'B' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 163 or (resid 164 \ and (name N or name CA or name C or name O or name CB )) or resid 165 or (resid \ 166 and (name N or name CA or name C or name O or name CB )) or resid 167 throug \ h 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 205 or (resid 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 through 235 or resid 239 or (resid 240 and (name N or \ name CA or name C or name O or name CB )) or resid 241 through 373 or (resid 374 \ and (name N or name CA or name C or name O or name CB )) or resid 375 through 4 \ 46 or (resid 447 and (name N or name CA or name C or name O or name CB )) or res \ id 448 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 483 or resid 490 through 501 or (resid 502 and (n \ ame N or name CA or name C or name O or name CB )) or resid 519 through 520 or ( \ resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 536 or (resid 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 779 or (resid 780 and (name N or name CA or name C or na \ me O or name CB )) or resid 781 through 1221 or resid 1301 through 1304)) selection = (chain 'C' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 130 or (resid 131 and (name N or n \ ame CA or name C or name O or name CB )) or resid 132 through 139 or (resid 140 \ and (name N or name CA or name C or name O or name CB )) or resid 141 through 18 \ 5 or (resid 186 and (name N or name CA or name C or name O or name CB )) or resi \ d 187 through 205 or (resid 206 and (name N or name CA or name C or name O or na \ me CB )) or resid 207 through 235 or resid 239 or (resid 240 and (name N or name \ CA or name C or name O or name CB )) or resid 241 through 244 or resid 254 thro \ ugh 311 or (resid 312 and (name N or name CA or name C or name O or name CB )) o \ r resid 313 through 363 or (resid 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 412 or (resid 413 and (name N or name CA or \ name C or name O or name CB )) or resid 414 through 491 or (resid 492 through 49 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 494 through \ 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) or re \ sid 538 through 553 or (resid 554 and (name N or name CA or name C or name O or \ name CB )) or resid 555 through 660 or (resid 661 and (name N or name CA or name \ C or name O or name CB )) or resid 662 through 779 or (resid 780 and (name N or \ name CA or name C or name O or name CB )) or resid 781 through 931 or (resid 93 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 933 through \ 1065 or (resid 1066 and (name N or name CA or name C or name O or name CB )) or \ resid 1067 through 1221 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 72.630 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.002 0.039 28498 Z= 0.141 Angle : 0.428 6.563 38831 Z= 0.223 Chirality : 0.041 0.273 4471 Planarity : 0.003 0.045 4969 Dihedral : 8.081 108.919 10531 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 1.19 % Allowed : 5.19 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -3.23 (0.12), residues: 3497 helix: -3.19 (0.11), residues: 642 sheet: -0.90 (0.19), residues: 696 loop : -2.33 (0.11), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.001 0.000 HIS B 175 PHE 0.016 0.001 PHE A 98 TYR 0.006 0.001 TYR C 56 ARG 0.001 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 556 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 THR cc_start: 0.5974 (p) cc_final: 0.5523 (p) REVERT: C 213 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 278 ASN cc_start: 0.8183 (m-40) cc_final: 0.7981 (m110) REVERT: C 402 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7368 (mm110) REVERT: C 464 ASP cc_start: 0.7908 (t0) cc_final: 0.7398 (t0) REVERT: C 915 ASP cc_start: 0.6923 (t70) cc_final: 0.6670 (t0) REVERT: A 52 LEU cc_start: 0.8888 (mm) cc_final: 0.8572 (mp) REVERT: A 579 SER cc_start: 0.8683 (p) cc_final: 0.8187 (m) REVERT: B 169 ILE cc_start: 0.8325 (pt) cc_final: 0.7794 (tt) REVERT: B 313 PRO cc_start: 0.5353 (Cg_endo) cc_final: 0.5081 (Cg_exo) REVERT: B 848 ASP cc_start: 0.7332 (m-30) cc_final: 0.7122 (m-30) REVERT: B 884 PHE cc_start: 0.6644 (m-10) cc_final: 0.6289 (m-80) outliers start: 37 outliers final: 14 residues processed: 585 average time/residue: 0.3753 time to fit residues: 350.0481 Evaluate side-chains 270 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 934 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 GLN C 847 ASN C 854 GLN C 856 GLN C 984 GLN C1001 GLN C1009 ASN C1030 GLN C1071 GLN A 26 ASN A 100 ASN A 160 HIS A 291 GLN A 353 ASN A 402 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 535 GLN A 587 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN A1046 GLN A1091 GLN A1126 ASN A1135 GLN B 100 ASN B 201 HIS B 243 ASN B 465 HIS B 535 GLN B 683 GLN B 804 GLN B 941 ASN B 998 ASN B1059 GLN B1091 GLN B1211 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28498 Z= 0.315 Angle : 0.615 9.581 38831 Z= 0.323 Chirality : 0.047 0.355 4471 Planarity : 0.004 0.048 4969 Dihedral : 6.052 59.705 4461 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.88 % Allowed : 8.69 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -2.04 (0.13), residues: 3497 helix: -0.37 (0.18), residues: 700 sheet: -0.74 (0.19), residues: 740 loop : -2.03 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.007 0.001 HIS C1145 PHE 0.027 0.002 PHE A 98 TYR 0.030 0.002 TYR C1219 ARG 0.004 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 266 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7604 (mm-40) REVERT: C 431 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7642 (pp) REVERT: C 464 ASP cc_start: 0.8262 (t0) cc_final: 0.7600 (t0) REVERT: C 501 TYR cc_start: 0.8177 (m-80) cc_final: 0.7860 (m-80) REVERT: C 566 PHE cc_start: 0.6947 (t80) cc_final: 0.5913 (m-80) REVERT: C 577 PHE cc_start: 0.7302 (m-10) cc_final: 0.7081 (m-80) REVERT: A 453 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.4481 (p90) REVERT: A 528 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: A 711 PHE cc_start: 0.7643 (m-80) cc_final: 0.7217 (m-80) REVERT: B 322 PRO cc_start: 0.7298 (Cg_exo) cc_final: 0.7015 (Cg_endo) REVERT: B 623 ASP cc_start: 0.7838 (t0) cc_final: 0.6926 (t0) REVERT: B 669 ILE cc_start: 0.9167 (mp) cc_final: 0.8877 (mt) REVERT: B 884 PHE cc_start: 0.7191 (m-10) cc_final: 0.6871 (m-80) REVERT: B 994 MET cc_start: 0.8509 (tpp) cc_final: 0.8122 (ttt) outliers start: 90 outliers final: 47 residues processed: 335 average time/residue: 0.3432 time to fit residues: 194.8725 Evaluate side-chains 257 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 207 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 836 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 890 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 30.0000 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 320 optimal weight: 0.0670 chunk 345 optimal weight: 0.7980 chunk 285 optimal weight: 0.7980 chunk 317 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 535 GLN C 584 ASN C 630 GLN C 876 HIS C 984 GLN C1001 GLN C1049 ASN C1071 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN B 100 ASN B 160 HIS B 552 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28498 Z= 0.203 Angle : 0.513 9.466 38831 Z= 0.271 Chirality : 0.044 0.249 4471 Planarity : 0.004 0.049 4969 Dihedral : 5.270 57.141 4452 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 9.78 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.55 (0.14), residues: 3497 helix: 0.64 (0.20), residues: 707 sheet: -0.53 (0.19), residues: 728 loop : -1.91 (0.12), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 174 HIS 0.004 0.001 HIS C 142 PHE 0.023 0.001 PHE A 566 TYR 0.017 0.001 TYR A 682 ARG 0.008 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 228 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 431 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 464 ASP cc_start: 0.8262 (t0) cc_final: 0.7578 (t0) REVERT: C 501 TYR cc_start: 0.8307 (m-80) cc_final: 0.7947 (m-80) REVERT: C 551 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7665 (mt) REVERT: C 566 PHE cc_start: 0.6915 (t80) cc_final: 0.5903 (m-80) REVERT: A 528 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5955 (m-80) REVERT: B 322 PRO cc_start: 0.7405 (Cg_exo) cc_final: 0.7134 (Cg_endo) REVERT: B 669 ILE cc_start: 0.9138 (mp) cc_final: 0.8933 (mt) REVERT: B 994 MET cc_start: 0.8500 (tpp) cc_final: 0.8178 (ttt) REVERT: B 1185 MET cc_start: 0.8728 (mmm) cc_final: 0.8478 (mtp) outliers start: 85 outliers final: 50 residues processed: 298 average time/residue: 0.3355 time to fit residues: 171.7825 Evaluate side-chains 263 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 1156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 0.0670 chunk 166 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 321 optimal weight: 0.0570 chunk 340 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 630 GLN C 984 GLN C1001 GLN C1071 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28498 Z= 0.141 Angle : 0.473 9.943 38831 Z= 0.248 Chirality : 0.043 0.242 4471 Planarity : 0.004 0.051 4969 Dihedral : 4.692 57.078 4451 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.44 % Allowed : 10.10 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.24 (0.14), residues: 3497 helix: 1.14 (0.21), residues: 721 sheet: -0.36 (0.19), residues: 728 loop : -1.81 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 174 HIS 0.003 0.001 HIS C 201 PHE 0.025 0.001 PHE A 566 TYR 0.019 0.001 TYR A 235 ARG 0.011 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 431 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7619 (pp) REVERT: C 464 ASP cc_start: 0.8255 (t0) cc_final: 0.7581 (t0) REVERT: C 551 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7563 (mt) REVERT: C 566 PHE cc_start: 0.6770 (t80) cc_final: 0.5838 (m-80) REVERT: C 1205 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6984 (mpp) REVERT: A 453 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4916 (p90) REVERT: B 34 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6942 (mmp-170) REVERT: B 87 THR cc_start: 0.8237 (t) cc_final: 0.8020 (t) REVERT: B 97 ASP cc_start: 0.8044 (t70) cc_final: 0.7802 (t0) REVERT: B 322 PRO cc_start: 0.7428 (Cg_exo) cc_final: 0.7162 (Cg_endo) REVERT: B 623 ASP cc_start: 0.7701 (t0) cc_final: 0.7474 (t0) REVERT: B 994 MET cc_start: 0.8484 (tpp) cc_final: 0.8088 (ttt) outliers start: 76 outliers final: 46 residues processed: 294 average time/residue: 0.3254 time to fit residues: 165.6838 Evaluate side-chains 252 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 202 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 290 optimal weight: 30.0000 chunk 235 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 630 GLN C 984 GLN C1129 HIS A 160 HIS A 847 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN B 100 ASN B 535 GLN B 838 ASN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 28498 Z= 0.414 Angle : 0.651 11.212 38831 Z= 0.340 Chirality : 0.048 0.312 4471 Planarity : 0.005 0.059 4969 Dihedral : 5.523 58.535 4451 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 3.49 % Allowed : 9.90 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.48 (0.14), residues: 3497 helix: 0.60 (0.20), residues: 743 sheet: -0.48 (0.19), residues: 749 loop : -1.88 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 575 HIS 0.009 0.002 HIS C1145 PHE 0.029 0.002 PHE B 713 TYR 0.028 0.002 TYR A 682 ARG 0.004 0.001 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 215 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: C 431 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (pp) REVERT: C 453 PHE cc_start: 0.6055 (t80) cc_final: 0.5540 (t80) REVERT: C 464 ASP cc_start: 0.8417 (t0) cc_final: 0.7572 (t0) REVERT: C 501 TYR cc_start: 0.8251 (m-80) cc_final: 0.7952 (m-80) REVERT: C 544 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: C 551 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7666 (mt) REVERT: C 800 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: C 1205 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7247 (mpp) REVERT: A 118 TYR cc_start: 0.6553 (m-80) cc_final: 0.6192 (m-80) REVERT: A 453 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5980 (p90) REVERT: A 1162 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8713 (pp) REVERT: B 100 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8225 (t0) REVERT: B 318 TYR cc_start: 0.7422 (m-80) cc_final: 0.7057 (m-80) outliers start: 109 outliers final: 67 residues processed: 299 average time/residue: 0.3108 time to fit residues: 160.5673 Evaluate side-chains 269 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 194 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 2.9990 chunk 306 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 340 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C1030 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28498 Z= 0.160 Angle : 0.515 11.046 38831 Z= 0.269 Chirality : 0.043 0.217 4471 Planarity : 0.004 0.055 4969 Dihedral : 4.973 56.536 4449 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 2.60 % Allowed : 11.35 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.25 (0.14), residues: 3497 helix: 0.98 (0.21), residues: 749 sheet: -0.50 (0.19), residues: 753 loop : -1.75 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.003 0.001 HIS C 201 PHE 0.018 0.001 PHE C 24 TYR 0.026 0.001 TYR B 84 ARG 0.004 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 216 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 431 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (pp) REVERT: C 453 PHE cc_start: 0.6051 (t80) cc_final: 0.5646 (t80) REVERT: C 464 ASP cc_start: 0.8381 (t0) cc_final: 0.7597 (t0) REVERT: C 501 TYR cc_start: 0.8181 (m-80) cc_final: 0.7896 (m-80) REVERT: C 551 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7534 (mt) REVERT: C 566 PHE cc_start: 0.7453 (t80) cc_final: 0.6273 (m-80) REVERT: C 800 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: C 1205 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: A 44 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8637 (mm) REVERT: A 118 TYR cc_start: 0.6606 (m-80) cc_final: 0.6271 (m-80) REVERT: A 453 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5742 (p90) REVERT: B 34 ARG cc_start: 0.7233 (mmm160) cc_final: 0.6957 (mmp-170) REVERT: B 318 TYR cc_start: 0.7286 (m-80) cc_final: 0.6951 (m-80) REVERT: B 623 ASP cc_start: 0.8312 (t0) cc_final: 0.7620 (t0) REVERT: B 994 MET cc_start: 0.8657 (tpp) cc_final: 0.8132 (ttt) outliers start: 81 outliers final: 54 residues processed: 277 average time/residue: 0.3371 time to fit residues: 160.7205 Evaluate side-chains 256 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 194 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN C 584 ASN C1030 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28498 Z= 0.219 Angle : 0.521 11.522 38831 Z= 0.272 Chirality : 0.044 0.297 4471 Planarity : 0.004 0.056 4969 Dihedral : 4.938 56.238 4449 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 2.69 % Allowed : 11.54 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.18 (0.14), residues: 3497 helix: 1.04 (0.21), residues: 749 sheet: -0.45 (0.19), residues: 753 loop : -1.70 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 575 HIS 0.005 0.001 HIS C 201 PHE 0.023 0.001 PHE A 566 TYR 0.020 0.001 TYR A 235 ARG 0.007 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 199 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 408 PHE cc_start: 0.7777 (m-80) cc_final: 0.7498 (m-80) REVERT: C 431 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7645 (pp) REVERT: C 453 PHE cc_start: 0.6003 (t80) cc_final: 0.5728 (t80) REVERT: C 464 ASP cc_start: 0.8371 (t0) cc_final: 0.7549 (t0) REVERT: C 501 TYR cc_start: 0.8220 (m-80) cc_final: 0.7940 (m-80) REVERT: C 551 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7618 (mt) REVERT: C 566 PHE cc_start: 0.7438 (t80) cc_final: 0.6273 (m-80) REVERT: C 800 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: C 1205 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: A 44 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8650 (mm) REVERT: A 453 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5903 (p90) REVERT: A 1162 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 34 ARG cc_start: 0.7225 (mmm160) cc_final: 0.6922 (mmp-170) REVERT: B 318 TYR cc_start: 0.7416 (m-80) cc_final: 0.7012 (m-80) REVERT: B 994 MET cc_start: 0.8682 (tpp) cc_final: 0.8178 (ttt) outliers start: 84 outliers final: 59 residues processed: 263 average time/residue: 0.3279 time to fit residues: 150.1831 Evaluate side-chains 260 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C1030 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28498 Z= 0.197 Angle : 0.510 12.343 38831 Z= 0.267 Chirality : 0.043 0.251 4471 Planarity : 0.004 0.054 4969 Dihedral : 4.836 55.754 4449 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 2.40 % Allowed : 11.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.09 (0.14), residues: 3497 helix: 1.19 (0.21), residues: 750 sheet: -0.41 (0.19), residues: 746 loop : -1.67 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 575 HIS 0.004 0.001 HIS C 201 PHE 0.024 0.001 PHE A 566 TYR 0.019 0.001 TYR A 235 ARG 0.007 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 200 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 MET cc_start: 0.8433 (mmm) cc_final: 0.7917 (ttm) REVERT: C 408 PHE cc_start: 0.7760 (m-80) cc_final: 0.7489 (m-80) REVERT: C 431 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7618 (pp) REVERT: C 453 PHE cc_start: 0.6060 (t80) cc_final: 0.5776 (t80) REVERT: C 464 ASP cc_start: 0.8326 (t0) cc_final: 0.7494 (t0) REVERT: C 501 TYR cc_start: 0.8185 (m-80) cc_final: 0.7936 (m-80) REVERT: C 551 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7567 (mt) REVERT: C 566 PHE cc_start: 0.7407 (t80) cc_final: 0.6340 (m-80) REVERT: C 800 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: C 1205 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7282 (mpp) REVERT: A 44 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 118 TYR cc_start: 0.6301 (m-80) cc_final: 0.6072 (m-80) REVERT: A 453 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5969 (p90) REVERT: A 1162 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 318 TYR cc_start: 0.7411 (m-80) cc_final: 0.7005 (m-80) REVERT: B 623 ASP cc_start: 0.8231 (t0) cc_final: 0.7327 (t0) REVERT: B 994 MET cc_start: 0.8664 (tpp) cc_final: 0.8178 (ttt) outliers start: 75 outliers final: 60 residues processed: 254 average time/residue: 0.3176 time to fit residues: 140.1926 Evaluate side-chains 254 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 0.8980 chunk 325 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 316 optimal weight: 0.8980 chunk 324 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 285 optimal weight: 0.7980 chunk 299 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28498 Z= 0.141 Angle : 0.488 12.618 38831 Z= 0.255 Chirality : 0.043 0.218 4471 Planarity : 0.004 0.052 4969 Dihedral : 4.624 55.441 4448 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.02 % Allowed : 12.40 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.95 (0.14), residues: 3497 helix: 1.33 (0.21), residues: 752 sheet: -0.33 (0.19), residues: 746 loop : -1.59 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS C 201 PHE 0.029 0.001 PHE A 566 TYR 0.017 0.001 TYR B 84 ARG 0.006 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 203 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 PHE cc_start: 0.7699 (m-80) cc_final: 0.7462 (m-80) REVERT: C 431 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7676 (pp) REVERT: C 453 PHE cc_start: 0.6025 (t80) cc_final: 0.5740 (t80) REVERT: C 464 ASP cc_start: 0.8324 (t0) cc_final: 0.7507 (t0) REVERT: C 501 TYR cc_start: 0.8128 (m-80) cc_final: 0.7919 (m-80) REVERT: C 551 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7565 (mt) REVERT: C 566 PHE cc_start: 0.7284 (t80) cc_final: 0.6211 (m-80) REVERT: C 800 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: C 1205 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: A 1162 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 318 TYR cc_start: 0.7312 (m-80) cc_final: 0.6947 (m-80) REVERT: B 623 ASP cc_start: 0.8132 (t0) cc_final: 0.7199 (t0) REVERT: B 994 MET cc_start: 0.8591 (tpp) cc_final: 0.8174 (ttt) outliers start: 63 outliers final: 51 residues processed: 250 average time/residue: 0.3166 time to fit residues: 138.0230 Evaluate side-chains 247 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 806 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 350 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28498 Z= 0.187 Angle : 0.504 12.734 38831 Z= 0.264 Chirality : 0.044 0.447 4471 Planarity : 0.004 0.053 4969 Dihedral : 4.727 55.252 4448 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 1.96 % Allowed : 12.69 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.95 (0.14), residues: 3497 helix: 1.38 (0.21), residues: 745 sheet: -0.36 (0.19), residues: 751 loop : -1.60 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 575 HIS 0.004 0.001 HIS B 201 PHE 0.029 0.001 PHE A 566 TYR 0.019 0.001 TYR A 729 ARG 0.006 0.000 ARG A1064 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 200 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 MET cc_start: 0.8022 (mtt) cc_final: 0.7622 (mtp) REVERT: C 238 MET cc_start: 0.8404 (mmm) cc_final: 0.7919 (ttm) REVERT: C 408 PHE cc_start: 0.7743 (m-80) cc_final: 0.7480 (m-80) REVERT: C 431 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7625 (pp) REVERT: C 453 PHE cc_start: 0.6078 (t80) cc_final: 0.5781 (t80) REVERT: C 464 ASP cc_start: 0.8311 (t0) cc_final: 0.7195 (t0) REVERT: C 465 HIS cc_start: 0.7853 (m-70) cc_final: 0.6896 (m-70) REVERT: C 551 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7607 (mt) REVERT: C 566 PHE cc_start: 0.7309 (t80) cc_final: 0.6263 (m-80) REVERT: C 800 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6873 (pm20) REVERT: C 1205 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: A 1162 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 84 TYR cc_start: 0.6862 (t80) cc_final: 0.6365 (t80) REVERT: B 318 TYR cc_start: 0.7314 (m-80) cc_final: 0.6898 (m-80) REVERT: B 623 ASP cc_start: 0.8204 (t0) cc_final: 0.7256 (t0) REVERT: B 994 MET cc_start: 0.8624 (tpp) cc_final: 0.8190 (ttt) outliers start: 61 outliers final: 54 residues processed: 246 average time/residue: 0.3154 time to fit residues: 135.5131 Evaluate side-chains 250 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 191 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 806 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 257 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 279 optimal weight: 0.0670 chunk 117 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.089449 restraints weight = 53852.161| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.89 r_work: 0.3140 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28498 Z= 0.219 Angle : 0.522 12.552 38831 Z= 0.273 Chirality : 0.044 0.438 4471 Planarity : 0.004 0.055 4969 Dihedral : 4.756 55.596 4446 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 2.37 % Allowed : 12.47 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.98 (0.14), residues: 3497 helix: 1.30 (0.21), residues: 749 sheet: -0.31 (0.19), residues: 746 loop : -1.63 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 575 HIS 0.004 0.001 HIS B 201 PHE 0.028 0.001 PHE A 566 TYR 0.024 0.001 TYR A 729 ARG 0.006 0.000 ARG A1064 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5852.82 seconds wall clock time: 105 minutes 28.02 seconds (6328.02 seconds total)