Starting phenix.real_space_refine on Wed Apr 10 19:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5b_27909/04_2024/8e5b_27909_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13098 2.51 5 N 3351 2.21 5 O 3743 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 689": "OD1" <-> "OD2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 907": "OD1" <-> "OD2" Residue "A PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1379": "OD1" <-> "OD2" Residue "D ASP 491": "OD1" <-> "OD2" Residue "D ASP 700": "OD1" <-> "OD2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D GLU 799": "OE1" <-> "OE2" Residue "D ASP 984": "OD1" <-> "OD2" Residue "D PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 339": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20310 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 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 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: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'BBI': 1, 'WG6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.09, per 1000 atoms: 0.55 Number of scatterers: 20310 At special positions: 0 Unit cell: (171.556, 170.442, 183.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 112 16.00 P 1 15.00 F 1 9.00 O 3743 8.00 N 3351 7.00 C 13098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 8.39 Conformation dependent library (CDL) restraints added in 3.5 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 15 sheets defined 49.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 126 through 145 removed outlier: 4.075A pdb=" N ILE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 178 removed outlier: 4.054A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.578A pdb=" N VAL A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.996A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 255 through 292 removed outlier: 3.917A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.758A pdb=" N HIS A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.759A pdb=" N LYS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.914A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.674A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 574 removed outlier: 4.086A pdb=" N GLN A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 606 removed outlier: 4.247A pdb=" N PHE A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 4.601A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE A 626 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 629 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.656A pdb=" N SER A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 672 Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.692A pdb=" N TYR A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 769 removed outlier: 3.536A pdb=" N ILE A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 733 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 734 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 735 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 736 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS A 738 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 739 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 740 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 741 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU A 748 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 750 " --> pdb=" O PHE A 747 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 753 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA A 756 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 757 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 760 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 766 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 767 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 768 " --> pdb=" O GLN A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 886 through 905 removed outlier: 4.137A pdb=" N ASN A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 940 removed outlier: 3.643A pdb=" N ALA A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 Processing helix chain 'A' and resid 980 through 994 removed outlier: 4.291A pdb=" N VAL A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) Proline residue: A 991 - end of helix removed outlier: 4.379A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1036 removed outlier: 5.221A pdb=" N ASN A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1087 through 1098 Processing helix chain 'A' and resid 1103 through 1111 Processing helix chain 'A' and resid 1126 through 1139 Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'A' and resid 1170 through 1180 removed outlier: 4.353A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A1179 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1180 " --> pdb=" O VAL A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1202 removed outlier: 4.740A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A1199 " --> pdb=" O GLN A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1224 removed outlier: 3.639A pdb=" N MET A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1258 Processing helix chain 'A' and resid 1261 through 1266 removed outlier: 4.172A pdb=" N PHE A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A1266 " --> pdb=" O LYS A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1261 through 1266' Processing helix chain 'A' and resid 1268 through 1283 removed outlier: 3.534A pdb=" N ILE A1282 " --> pdb=" O ILE A1278 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1315 through 1332 removed outlier: 3.523A pdb=" N ARG A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A1322 " --> pdb=" O PHE A1318 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A1323 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A1327 " --> pdb=" O VAL A1323 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A1328 " --> pdb=" O MET A1324 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1330 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A1332 " --> pdb=" O LYS A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1315 through 1332' Processing helix chain 'A' and resid 1336 through 1349 Processing helix chain 'A' and resid 1351 through 1372 removed outlier: 3.653A pdb=" N LEU A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1415 Processing helix chain 'A' and resid 1438 through 1465 removed outlier: 3.691A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1442 " --> pdb=" O PHE A1439 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1446 " --> pdb=" O TYR A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1471 No H-bonds generated for 'chain 'A' and resid 1469 through 1471' Processing helix chain 'A' and resid 1479 through 1492 removed outlier: 3.616A pdb=" N GLU A1491 " --> pdb=" O ARG A1487 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1511 Processing helix chain 'A' and resid 1527 through 1533 removed outlier: 3.553A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1557 removed outlier: 4.146A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1575 Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.579A pdb=" N GLU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.784A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.560A pdb=" N ARG D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 199 removed outlier: 3.522A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU D 189 " --> pdb=" O TRP D 185 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.876A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.975A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.558A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 406 removed outlier: 3.592A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.487A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.562A pdb=" N ASP D 428 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 430' Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.866A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.788A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 569 through 579 Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.102A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 3.829A pdb=" N PHE D 653 " --> pdb=" O PRO D 650 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 655 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 650 through 656' Processing helix chain 'D' and resid 679 through 687 Processing helix chain 'D' and resid 700 through 718 removed outlier: 4.093A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 717 " --> pdb=" O ASN D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 4.091A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.822A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.556A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 825 " --> pdb=" O TRP D 821 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 826 " --> pdb=" O ILE D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 removed outlier: 3.691A pdb=" N ASN D 888 " --> pdb=" O ARG D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing helix chain 'C' and resid 39 through 57 removed outlier: 3.676A pdb=" N LYS C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N HIS C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 removed outlier: 3.512A pdb=" N LEU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 191 through 207 removed outlier: 3.584A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 247 through 263 removed outlier: 3.832A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.792A pdb=" N ALA C 281 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.576A pdb=" N GLN C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 326 removed outlier: 3.729A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 342 through 359 removed outlier: 3.708A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id= B, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= C, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.620A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 298 through 300 removed outlier: 7.024A pdb=" N ASN D 355 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU D 255 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE D 357 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU D 257 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET D 359 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP D 259 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE D 361 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG D 383 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU D 360 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE D 385 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR D 362 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE D 387 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR D 409 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER D 388 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR D 411 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= F, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= G, first strand: chain 'D' and resid 658 through 661 removed outlier: 3.932A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 774 through 776 removed outlier: 3.852A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 990 through 994 removed outlier: 6.603A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 892 through 899 Processing sheet with id= K, first strand: chain 'D' and resid 902 through 905 removed outlier: 3.502A pdb=" N GLN D 972 " --> pdb=" O CYS D 904 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 63 through 65 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.464A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.903A pdb=" N LEU C 266 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR C 215 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL C 268 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= O 802 hydrogen bonds defined for protein. 2130 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: 7.19 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 6548 1.37 - 1.55: 14008 1.55 - 1.74: 12 1.74 - 1.92: 176 1.92 - 2.11: 2 Bond restraints: 20746 Sorted by residual: bond pdb=" C14 WG6 A2202 " pdb=" C15 WG6 A2202 " ideal model delta sigma weight residual 1.327 1.564 -0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C14 WG6 A2202 " pdb=" O18 WG6 A2202 " ideal model delta sigma weight residual 1.648 1.437 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C13 WG6 A2202 " pdb=" C14 WG6 A2202 " ideal model delta sigma weight residual 1.487 1.660 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C17 WG6 A2202 " pdb=" N19 WG6 A2202 " ideal model delta sigma weight residual 1.447 1.609 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C17 WG6 A2202 " pdb=" O18 WG6 A2202 " ideal model delta sigma weight residual 1.317 1.434 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 20741 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.46: 491 106.46 - 113.66: 11500 113.66 - 120.87: 9991 120.87 - 128.08: 5989 128.08 - 135.28: 133 Bond angle restraints: 28104 Sorted by residual: angle pdb=" C31 WG6 A2202 " pdb=" O30 WG6 A2202 " pdb=" P10 WG6 A2202 " ideal model delta sigma weight residual 118.45 132.54 -14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 113.53 109.37 4.16 9.80e-01 1.04e+00 1.80e+01 angle pdb=" CB MET A1369 " pdb=" CG MET A1369 " pdb=" SD MET A1369 " ideal model delta sigma weight residual 112.70 102.64 10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C13 WG6 A2202 " pdb=" O12 WG6 A2202 " pdb=" P10 WG6 A2202 " ideal model delta sigma weight residual 118.50 128.24 -9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N ASN C 140 " pdb=" CA ASN C 140 " pdb=" C ASN C 140 " ideal model delta sigma weight residual 109.81 116.46 -6.65 2.21e+00 2.05e-01 9.04e+00 ... (remaining 28099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.73: 11687 23.73 - 47.47: 767 47.47 - 71.20: 89 71.20 - 94.94: 35 94.94 - 118.67: 15 Dihedral angle restraints: 12593 sinusoidal: 5276 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 175.55 -82.55 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual 93.00 42.65 50.35 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 12590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.184: 3200 1.184 - 2.369: 0 2.369 - 3.553: 0 3.553 - 4.737: 0 4.737 - 5.921: 1 Chirality restraints: 3201 Sorted by residual: chirality pdb=" C16 WG6 A2202 " pdb=" C15 WG6 A2202 " pdb=" C17 WG6 A2202 " pdb=" C27 WG6 A2202 " both_signs ideal model delta sigma weight residual False 2.82 -3.10 5.92 2.00e-01 2.50e+01 8.77e+02 chirality pdb=" P10 WG6 A2202 " pdb=" O11 WG6 A2202 " pdb=" O12 WG6 A2202 " pdb=" O30 WG6 A2202 " both_signs ideal model delta sigma weight residual True 3.19 -3.59 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3198 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 348 " -0.020 2.00e-02 2.50e+03 1.89e-02 4.48e+00 pdb=" CG ASN D 348 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN D 348 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN D 348 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 140 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO C 141 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 516 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO D 517 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 517 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 517 " 0.025 5.00e-02 4.00e+02 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.74: 1404 2.74 - 3.29: 21552 3.29 - 3.85: 33749 3.85 - 4.40: 41102 4.40 - 4.96: 69828 Nonbonded interactions: 167635 Sorted by model distance: nonbonded pdb=" OE2 GLU D 182 " pdb=" OG SER D 210 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR D 450 " pdb=" OG1 THR D 461 " model vdw 2.181 2.440 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.196 2.440 nonbonded pdb=" O ALA A 519 " pdb=" OG SER A 522 " model vdw 2.220 2.440 nonbonded pdb=" OG SER A 911 " pdb=" OD2 ASP A1426 " model vdw 2.234 2.440 ... (remaining 167630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 1.120 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: 0.010 Extract box with map and model: 6.150 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 56.870 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 20746 Z= 0.278 Angle : 0.585 14.087 28104 Z= 0.286 Chirality : 0.114 5.921 3201 Planarity : 0.003 0.052 3555 Dihedral : 16.028 118.669 7827 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.27 (0.17), residues: 2472 helix: 0.69 (0.15), residues: 1172 sheet: -0.07 (0.33), residues: 270 loop : -1.18 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 PHE 0.020 0.001 PHE A1343 TYR 0.013 0.001 TYR A1443 ARG 0.003 0.000 ARG A1378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: A 730 ILE cc_start: 0.8839 (pt) cc_final: 0.8602 (pt) REVERT: D 268 THR cc_start: 0.9342 (t) cc_final: 0.9033 (m) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3125 time to fit residues: 138.6431 Evaluate side-chains 224 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN ** D 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20746 Z= 0.165 Angle : 0.620 29.706 28104 Z= 0.289 Chirality : 0.053 1.856 3201 Planarity : 0.004 0.050 3555 Dihedral : 10.125 107.854 3012 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.68 % Allowed : 7.19 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.25 (0.17), residues: 2472 helix: 0.75 (0.15), residues: 1196 sheet: -0.12 (0.32), residues: 276 loop : -1.27 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1199 HIS 0.002 0.000 HIS D1004 PHE 0.019 0.001 PHE A 202 TYR 0.022 0.001 TYR D 719 ARG 0.002 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 2.443 Fit side-chains REVERT: A 170 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6847 (mp) REVERT: A 934 ILE cc_start: 0.8364 (pt) cc_final: 0.8078 (mt) REVERT: A 1278 ILE cc_start: 0.7842 (mm) cc_final: 0.7599 (mm) REVERT: A 1344 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8810 (mp) REVERT: D 41 GLN cc_start: 0.8191 (pp30) cc_final: 0.7419 (pp30) REVERT: D 77 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: D 859 LEU cc_start: 0.8393 (tt) cc_final: 0.8127 (tp) outliers start: 15 outliers final: 8 residues processed: 259 average time/residue: 0.3034 time to fit residues: 126.3887 Evaluate side-chains 243 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 1045 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 224 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN A1017 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 20746 Z= 0.460 Angle : 0.738 29.702 28104 Z= 0.354 Chirality : 0.058 1.832 3201 Planarity : 0.005 0.049 3555 Dihedral : 9.142 102.954 3012 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.17 % Allowed : 11.13 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.70 (0.17), residues: 2472 helix: 0.36 (0.15), residues: 1198 sheet: -0.29 (0.31), residues: 282 loop : -1.48 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1103 HIS 0.006 0.001 HIS A 544 PHE 0.021 0.002 PHE A 293 TYR 0.021 0.002 TYR D 764 ARG 0.004 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6782 (mp) REVERT: A 254 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8095 (m) REVERT: A 285 TYR cc_start: 0.9153 (m-80) cc_final: 0.8895 (m-80) REVERT: A 293 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7242 (p90) REVERT: A 1150 PHE cc_start: 0.8209 (t80) cc_final: 0.7997 (t80) REVERT: A 1344 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8975 (mp) REVERT: D 77 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: D 268 THR cc_start: 0.9340 (t) cc_final: 0.9008 (m) REVERT: D 753 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: D 859 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8264 (tp) REVERT: D 1009 MET cc_start: 0.8039 (tpt) cc_final: 0.7715 (tpt) outliers start: 48 outliers final: 29 residues processed: 278 average time/residue: 0.3048 time to fit residues: 136.5961 Evaluate side-chains 272 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 772 ASN Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20746 Z= 0.242 Angle : 0.631 29.441 28104 Z= 0.296 Chirality : 0.054 1.820 3201 Planarity : 0.004 0.046 3555 Dihedral : 8.419 100.422 3012 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 13.85 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.59 (0.17), residues: 2472 helix: 0.51 (0.15), residues: 1191 sheet: -0.28 (0.31), residues: 280 loop : -1.49 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1199 HIS 0.003 0.001 HIS D 306 PHE 0.014 0.001 PHE D 513 TYR 0.013 0.001 TYR D1068 ARG 0.002 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6624 (mp) REVERT: A 285 TYR cc_start: 0.9144 (m-80) cc_final: 0.8887 (m-80) REVERT: A 293 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7303 (p90) REVERT: A 1185 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.5351 (tt) REVERT: A 1278 ILE cc_start: 0.7879 (mm) cc_final: 0.7649 (mm) REVERT: A 1344 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8957 (mp) REVERT: D 77 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: D 268 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8909 (m) REVERT: D 506 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8819 (mt) REVERT: D 859 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8171 (tp) outliers start: 43 outliers final: 24 residues processed: 270 average time/residue: 0.2995 time to fit residues: 131.0777 Evaluate side-chains 266 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 122 optimal weight: 0.0770 chunk 216 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20746 Z= 0.212 Angle : 0.612 29.291 28104 Z= 0.285 Chirality : 0.053 1.828 3201 Planarity : 0.004 0.046 3555 Dihedral : 7.936 98.242 3012 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.26 % Allowed : 14.84 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.53 (0.17), residues: 2472 helix: 0.58 (0.15), residues: 1199 sheet: -0.28 (0.31), residues: 276 loop : -1.50 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 441 HIS 0.002 0.000 HIS D 306 PHE 0.013 0.001 PHE D 513 TYR 0.011 0.001 TYR A 146 ARG 0.002 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 2.330 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6642 (mp) REVERT: A 202 PHE cc_start: 0.7134 (p90) cc_final: 0.6787 (p90) REVERT: A 285 TYR cc_start: 0.9142 (m-80) cc_final: 0.8878 (m-80) REVERT: A 293 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.7202 (p90) REVERT: A 1185 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5373 (tt) REVERT: A 1278 ILE cc_start: 0.7850 (mm) cc_final: 0.7638 (mm) REVERT: A 1344 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8963 (mp) REVERT: D 77 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: D 268 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8895 (m) REVERT: D 859 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8134 (tp) REVERT: C 196 MET cc_start: 0.6485 (tpt) cc_final: 0.5698 (tpp) REVERT: C 358 ARG cc_start: 0.4463 (tpt90) cc_final: 0.2906 (mmt180) outliers start: 50 outliers final: 31 residues processed: 272 average time/residue: 0.2922 time to fit residues: 128.7786 Evaluate side-chains 274 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20746 Z= 0.159 Angle : 0.587 29.112 28104 Z= 0.271 Chirality : 0.052 1.835 3201 Planarity : 0.003 0.046 3555 Dihedral : 7.410 94.622 3012 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 1.90 % Allowed : 15.93 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.37 (0.17), residues: 2472 helix: 0.75 (0.15), residues: 1196 sheet: -0.26 (0.31), residues: 276 loop : -1.45 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1199 HIS 0.002 0.000 HIS A 298 PHE 0.012 0.001 PHE D 513 TYR 0.010 0.001 TYR A 146 ARG 0.002 0.000 ARG D1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 2.552 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7615 (tt) cc_final: 0.7409 (pt) REVERT: A 170 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6749 (mp) REVERT: A 202 PHE cc_start: 0.7234 (p90) cc_final: 0.6922 (p90) REVERT: A 1344 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8942 (mp) REVERT: D 77 GLN cc_start: 0.7955 (tp40) cc_final: 0.7695 (mp10) REVERT: D 268 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8879 (m) REVERT: D 506 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8841 (mt) REVERT: D 859 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (tp) REVERT: D 1009 MET cc_start: 0.7953 (tpt) cc_final: 0.7659 (tpt) REVERT: C 196 MET cc_start: 0.6145 (tpt) cc_final: 0.5129 (tpp) outliers start: 42 outliers final: 26 residues processed: 270 average time/residue: 0.2955 time to fit residues: 129.8160 Evaluate side-chains 266 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN A1114 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20746 Z= 0.185 Angle : 0.597 29.123 28104 Z= 0.276 Chirality : 0.053 1.834 3201 Planarity : 0.004 0.046 3555 Dihedral : 7.168 90.390 3012 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 16.43 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.36 (0.17), residues: 2472 helix: 0.78 (0.15), residues: 1191 sheet: -0.25 (0.32), residues: 276 loop : -1.46 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 PHE 0.022 0.001 PHE D1015 TYR 0.012 0.001 TYR D 644 ARG 0.002 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 2.409 Fit side-chains revert: symmetry clash REVERT: A 130 ILE cc_start: 0.7614 (tt) cc_final: 0.7410 (pt) REVERT: A 170 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6779 (mp) REVERT: A 202 PHE cc_start: 0.7231 (p90) cc_final: 0.6928 (p90) REVERT: A 293 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7110 (p90) REVERT: A 1344 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (mp) REVERT: D 77 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: D 268 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8879 (m) REVERT: D 506 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (mt) REVERT: D 719 TYR cc_start: 0.7723 (t80) cc_final: 0.7490 (t80) REVERT: D 859 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8079 (tp) REVERT: C 196 MET cc_start: 0.5846 (tpt) cc_final: 0.4936 (tpp) REVERT: C 358 ARG cc_start: 0.4267 (tpt90) cc_final: 0.2711 (mmt180) outliers start: 49 outliers final: 35 residues processed: 263 average time/residue: 0.3050 time to fit residues: 130.5561 Evaluate side-chains 274 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 232 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 152 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 20746 Z= 0.151 Angle : 0.579 28.973 28104 Z= 0.266 Chirality : 0.052 1.841 3201 Planarity : 0.003 0.046 3555 Dihedral : 6.782 84.484 3012 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.22 % Allowed : 16.88 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.23 (0.17), residues: 2472 helix: 0.90 (0.15), residues: 1194 sheet: -0.25 (0.32), residues: 276 loop : -1.41 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1199 HIS 0.002 0.000 HIS D 306 PHE 0.022 0.001 PHE D1015 TYR 0.009 0.001 TYR A1364 ARG 0.002 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 247 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6789 (mp) REVERT: A 202 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7023 (p90) REVERT: A 293 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7114 (p90) REVERT: A 1344 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8921 (mp) REVERT: D 77 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: D 268 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8861 (m) REVERT: D 506 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8697 (mt) REVERT: D 859 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8126 (tp) REVERT: D 1009 MET cc_start: 0.7921 (tpt) cc_final: 0.7644 (tpt) REVERT: C 196 MET cc_start: 0.5734 (tpt) cc_final: 0.5030 (tpp) REVERT: C 358 ARG cc_start: 0.4559 (tpt90) cc_final: 0.2968 (mmt180) outliers start: 49 outliers final: 35 residues processed: 276 average time/residue: 0.3093 time to fit residues: 136.9464 Evaluate side-chains 277 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 chunk 134 optimal weight: 0.0270 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20746 Z= 0.173 Angle : 0.591 28.995 28104 Z= 0.272 Chirality : 0.052 1.839 3201 Planarity : 0.004 0.046 3555 Dihedral : 6.646 78.215 3012 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.99 % Allowed : 17.51 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2472 helix: 0.90 (0.15), residues: 1196 sheet: -0.29 (0.32), residues: 276 loop : -1.42 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 441 HIS 0.002 0.000 HIS D 306 PHE 0.021 0.001 PHE D1015 TYR 0.014 0.001 TYR D 644 ARG 0.003 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 202 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7133 (p90) REVERT: A 293 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7144 (p90) REVERT: A 1344 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8907 (mp) REVERT: D 77 GLN cc_start: 0.7967 (tp40) cc_final: 0.7698 (mp10) REVERT: D 254 MET cc_start: 0.8320 (ttt) cc_final: 0.8075 (ttt) REVERT: D 268 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8876 (m) REVERT: D 506 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8705 (mt) REVERT: D 859 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8071 (tp) REVERT: D 1009 MET cc_start: 0.7921 (tpt) cc_final: 0.7648 (tpt) REVERT: C 196 MET cc_start: 0.6340 (tpt) cc_final: 0.5490 (tpp) REVERT: C 358 ARG cc_start: 0.4307 (tpt90) cc_final: 0.2741 (mmt180) outliers start: 44 outliers final: 35 residues processed: 263 average time/residue: 0.2916 time to fit residues: 125.4326 Evaluate side-chains 275 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.0980 chunk 236 optimal weight: 0.0570 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 0.0970 chunk 248 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 20746 Z= 0.139 Angle : 0.579 28.831 28104 Z= 0.265 Chirality : 0.052 1.846 3201 Planarity : 0.004 0.053 3555 Dihedral : 6.359 69.057 3012 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.86 % Allowed : 18.05 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.07 (0.17), residues: 2472 helix: 1.07 (0.16), residues: 1184 sheet: -0.33 (0.32), residues: 269 loop : -1.29 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 441 HIS 0.001 0.000 HIS D 306 PHE 0.021 0.001 PHE D1015 TYR 0.014 0.001 TYR D 644 ARG 0.002 0.000 ARG D1029 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 2.560 Fit side-chains revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6872 (mp) REVERT: A 202 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7120 (p90) REVERT: A 293 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7122 (p90) REVERT: A 1344 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 254 MET cc_start: 0.8169 (ttt) cc_final: 0.7950 (ttt) REVERT: D 268 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8876 (m) REVERT: D 506 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8639 (mt) REVERT: D 859 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8056 (tp) REVERT: D 1009 MET cc_start: 0.7922 (tpt) cc_final: 0.7644 (tpt) REVERT: C 196 MET cc_start: 0.6301 (tpt) cc_final: 0.5429 (tpp) outliers start: 41 outliers final: 31 residues processed: 268 average time/residue: 0.2958 time to fit residues: 129.5200 Evaluate side-chains 271 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1371 MET Chi-restraints excluded: chain A residue 1435 CYS Chi-restraints excluded: chain A residue 1532 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 861 MET Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain C residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 182 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137947 restraints weight = 25702.635| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.40 r_work: 0.3097 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 20746 Z= 0.159 Angle : 0.583 28.869 28104 Z= 0.268 Chirality : 0.052 1.843 3201 Planarity : 0.004 0.056 3555 Dihedral : 6.260 68.092 3012 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.04 % Allowed : 17.87 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.07 (0.17), residues: 2472 helix: 1.07 (0.16), residues: 1186 sheet: -0.38 (0.32), residues: 271 loop : -1.28 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1199 HIS 0.001 0.000 HIS D 306 PHE 0.020 0.001 PHE D1015 TYR 0.015 0.001 TYR D 719 ARG 0.007 0.000 ARG D 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.79 seconds wall clock time: 83 minutes 47.88 seconds (5027.88 seconds total)