Starting phenix.real_space_refine on Sun Feb 18 17:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdz_13928/02_2024/7qdz_13928.pdb" } resolution = 3.6 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= 0.002 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 14295 2.51 5 N 3914 2.21 5 O 4269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1041": "NH1" <-> "NH2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A TYR 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 757": "OE1" <-> "OE2" Residue "B ASP 781": "OD1" <-> "OD2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B ASP 891": "OD1" <-> "OD2" Residue "B ARG 918": "NH1" <-> "NH2" Residue "B TYR 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B ASP 1017": "OD1" <-> "OD2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1250": "OD1" <-> "OD2" Residue "B TYR 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1314": "OE1" <-> "OE2" Residue "B GLU 1325": "OE1" <-> "OE2" Residue "B ARG 1367": "NH1" <-> "NH2" Residue "B TYR 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1424": "NH1" <-> "NH2" Residue "B ARG 1503": "NH1" <-> "NH2" Residue "B ARG 1507": "NH1" <-> "NH2" Residue "B TYR 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1523": "NH1" <-> "NH2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B ARG 1560": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D ASP 260": "OD1" <-> "OD2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 302": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 8674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 8674 Classifications: {'peptide': 1145} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 24, 'TRANS': 1120} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 8, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 8, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 202 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 106 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 12 Time building chain proxies: 11.59, per 1000 atoms: 0.51 Number of scatterers: 22591 At special positions: 0 Unit cell: (132.787, 171.942, 171.091, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 6 15.00 O 4269 8.00 N 3914 7.00 C 14295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 3.8 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5476 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 22 sheets defined 51.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.345A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.712A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.526A pdb=" N LEU A 91 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 4.066A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.171A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.508A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.614A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.518A pdb=" N TYR A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.026A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.990A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.592A pdb=" N THR A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.061A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.569A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 662 through 669 removed outlier: 4.136A pdb=" N VAL A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.890A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.803A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 761 through 768 removed outlier: 4.231A pdb=" N MET A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 3.964A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.867A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.282A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 992 through 1010 removed outlier: 3.542A pdb=" N VAL A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1019 through 1045 removed outlier: 3.848A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.570A pdb=" N LEU A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 3.947A pdb=" N ALA A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 3.825A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1128 through 1151 removed outlier: 3.914A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.816A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 removed outlier: 4.089A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 3.516A pdb=" N SER A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1211 " --> pdb=" O CYS A1207 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.884A pdb=" N THR A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.615A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.709A pdb=" N LEU B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 461 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 527 through 541 removed outlier: 3.743A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.716A pdb=" N LYS B 557 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 removed outlier: 4.110A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.556A pdb=" N ALA B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.545A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.688A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.887A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.512A pdb=" N ALA B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.685A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.684A pdb=" N ALA B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.262A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.662A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.510A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.649A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 874 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.849A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.553A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 979 through 993 removed outlier: 3.832A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1010 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.576A pdb=" N THR B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.942A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1102 removed outlier: 3.730A pdb=" N GLN B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1138 through 1152 removed outlier: 3.604A pdb=" N ALA B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.613A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.668A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.200A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 4.041A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 Processing helix chain 'B' and resid 1361 through 1371 removed outlier: 3.522A pdb=" N LEU B1365 " --> pdb=" O ALA B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1396 Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.545A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1434 removed outlier: 3.541A pdb=" N ALA B1419 " --> pdb=" O MET B1415 " (cutoff:3.500A) Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.795A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 removed outlier: 3.557A pdb=" N VAL B1484 " --> pdb=" O CYS B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.856A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1549 Processing helix chain 'B' and resid 1552 through 1563 removed outlier: 4.116A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.705A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 8.145A pdb=" N MET A 398 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 358 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG A 355 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ILE A 421 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 357 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 removed outlier: 6.686A pdb=" N HIS A 489 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A 633 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AA7, first strand: chain 'A' and resid 913 through 920 removed outlier: 3.554A pdb=" N ASP A 914 " --> pdb=" O CYS A 877 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A 877 " --> pdb=" O ASP A 914 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR A 872 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 876 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 856 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASP A 878 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 12.977A pdb=" N ASN A 854 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS A 848 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 925 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 7.003A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 3.596A pdb=" N SER C 21 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 56 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.740A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.554A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 176 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 182 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.668A pdb=" N LEU C 205 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 215 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.554A pdb=" N ASN C 237 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.358A pdb=" N VAL D 44 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER D 59 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 46 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.984A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 156 removed outlier: 4.019A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.606A pdb=" N SER D 195 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.867A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 277 through 282 1140 hydrogen bonds defined for protein. 3321 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: 8.41 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6931 1.33 - 1.46: 3981 1.46 - 1.58: 11962 1.58 - 1.70: 11 1.70 - 1.82: 168 Bond restraints: 23053 Sorted by residual: bond pdb=" SD MET C 191 " pdb=" CE MET C 191 " ideal model delta sigma weight residual 1.791 1.737 0.054 2.50e-02 1.60e+03 4.73e+00 bond pdb=" CG LEU B 688 " pdb=" CD1 LEU B 688 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.87e+00 bond pdb=" CB VAL B 973 " pdb=" CG2 VAL B 973 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.08e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" C SER B1266 " pdb=" N PRO B1267 " ideal model delta sigma weight residual 1.339 1.282 0.057 3.40e-02 8.65e+02 2.83e+00 ... (remaining 23048 not shown) Histogram of bond angle deviations from ideal: 92.14 - 100.52: 22 100.52 - 108.91: 1856 108.91 - 117.29: 15098 117.29 - 125.68: 13909 125.68 - 134.06: 421 Bond angle restraints: 31306 Sorted by residual: angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 112.05 -8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.21 -7.96 1.05e+00 9.07e-01 5.75e+01 angle pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " ideal model delta sigma weight residual 118.09 114.12 3.97 8.20e-01 1.49e+00 2.35e+01 angle pdb=" N GLU B 674 " pdb=" CA GLU B 674 " pdb=" CB GLU B 674 " ideal model delta sigma weight residual 110.16 116.28 -6.12 1.48e+00 4.57e-01 1.71e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 31301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 12389 17.59 - 35.18: 1242 35.18 - 52.77: 188 52.77 - 70.36: 57 70.36 - 87.95: 22 Dihedral angle restraints: 13898 sinusoidal: 5417 harmonic: 8481 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N LYS C 140 " pdb=" CA LYS C 140 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2529 0.053 - 0.106: 860 0.106 - 0.160: 166 0.160 - 0.213: 22 0.213 - 0.266: 6 Chirality restraints: 3583 Sorted by residual: chirality pdb=" CG LEU A 628 " pdb=" CB LEU A 628 " pdb=" CD1 LEU A 628 " pdb=" CD2 LEU A 628 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU C 43 " pdb=" CB LEU C 43 " pdb=" CD1 LEU C 43 " pdb=" CD2 LEU C 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CG LEU C 84 " pdb=" CB LEU C 84 " pdb=" CD1 LEU C 84 " pdb=" CD2 LEU C 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3580 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 640 " -0.082 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO A 641 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1463 " -0.030 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP B1463 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B1463 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1463 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1463 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1463 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1463 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1463 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1463 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1463 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1180 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A1181 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A1181 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1181 " 0.052 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 228 2.53 - 3.12: 18653 3.12 - 3.72: 35302 3.72 - 4.31: 47227 4.31 - 4.90: 79446 Nonbonded interactions: 180856 Sorted by model distance: nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 1.941 2.440 nonbonded pdb=" O ALA A 666 " pdb=" NH1 ARG A 703 " model vdw 2.042 2.520 nonbonded pdb=" OE1 GLU A 23 " pdb=" OG SER A 41 " model vdw 2.051 2.440 nonbonded pdb=" O THR B1392 " pdb=" OG SER B1395 " model vdw 2.070 2.440 nonbonded pdb=" NH1 ARG A 576 " pdb=" OP1 U E 2 " model vdw 2.088 2.520 ... (remaining 180851 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 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.980 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 58.070 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.007 0.074 23053 Z= 0.454 Angle : 0.982 14.268 31306 Z= 0.539 Chirality : 0.054 0.266 3583 Planarity : 0.007 0.124 4009 Dihedral : 14.683 87.948 8422 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2908 helix: 0.90 (0.14), residues: 1405 sheet: -1.74 (0.26), residues: 349 loop : -3.25 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP B1463 HIS 0.013 0.002 HIS A 636 PHE 0.049 0.003 PHE A 665 TYR 0.041 0.003 TYR B 517 ARG 0.012 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.435 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.6923 (p0) cc_final: 0.6523 (p0) REVERT: A 490 TYR cc_start: 0.8149 (m-80) cc_final: 0.7744 (m-80) REVERT: A 671 MET cc_start: 0.5113 (tpt) cc_final: 0.4650 (ttt) REVERT: A 734 MET cc_start: 0.8665 (tmm) cc_final: 0.8144 (tmm) REVERT: A 1193 GLU cc_start: 0.5640 (mp0) cc_final: 0.4984 (mp0) REVERT: B 1023 ILE cc_start: 0.9125 (mm) cc_final: 0.8910 (mm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3014 time to fit residues: 91.4005 Evaluate side-chains 136 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 75 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 87 optimal weight: 0.1980 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 617 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23053 Z= 0.300 Angle : 0.715 12.326 31306 Z= 0.372 Chirality : 0.044 0.199 3583 Planarity : 0.005 0.075 4009 Dihedral : 6.678 76.303 3223 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.91 % Favored : 91.06 % Rotamer: Outliers : 0.80 % Allowed : 9.12 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2908 helix: 1.18 (0.14), residues: 1422 sheet: -1.44 (0.29), residues: 319 loop : -2.91 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B1463 HIS 0.009 0.002 HIS A 636 PHE 0.032 0.002 PHE B1316 TYR 0.026 0.002 TYR B 608 ARG 0.006 0.001 ARG B1528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7083 (p0) cc_final: 0.6671 (p0) REVERT: A 490 TYR cc_start: 0.8014 (m-80) cc_final: 0.7685 (m-80) REVERT: A 671 MET cc_start: 0.4628 (tpt) cc_final: 0.4307 (ttt) REVERT: A 681 MET cc_start: 0.6442 (mmp) cc_final: 0.6233 (tpp) REVERT: A 726 MET cc_start: 0.4553 (ppp) cc_final: 0.4209 (tmm) REVERT: A 734 MET cc_start: 0.8687 (tmm) cc_final: 0.8115 (tmm) REVERT: A 822 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: A 1193 GLU cc_start: 0.6033 (mp0) cc_final: 0.5278 (mp0) REVERT: B 517 TYR cc_start: 0.7534 (m-80) cc_final: 0.7299 (m-80) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.2950 time to fit residues: 83.4574 Evaluate side-chains 149 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 219 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 285 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS ** A 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN B 942 GLN ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1558 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 23053 Z= 0.369 Angle : 0.729 13.218 31306 Z= 0.378 Chirality : 0.045 0.169 3583 Planarity : 0.005 0.067 4009 Dihedral : 6.661 79.935 3223 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.78 % Rotamer: Outliers : 2.15 % Allowed : 14.23 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.16), residues: 2908 helix: 1.16 (0.14), residues: 1426 sheet: -1.36 (0.29), residues: 322 loop : -2.84 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1463 HIS 0.010 0.002 HIS A 636 PHE 0.024 0.002 PHE A1020 TYR 0.035 0.002 TYR D 162 ARG 0.006 0.001 ARG B1528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TYR cc_start: 0.8053 (m-80) cc_final: 0.7849 (m-80) REVERT: A 671 MET cc_start: 0.4646 (tpt) cc_final: 0.4339 (ttt) REVERT: A 734 MET cc_start: 0.8792 (tmm) cc_final: 0.8289 (tmm) REVERT: A 1038 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 1193 GLU cc_start: 0.6176 (mp0) cc_final: 0.5421 (mp0) REVERT: B 517 TYR cc_start: 0.7381 (m-80) cc_final: 0.6971 (m-80) REVERT: B 803 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (pp) REVERT: B 886 MET cc_start: 0.8392 (tmm) cc_final: 0.8157 (tmm) REVERT: B 1475 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9156 (pp) outliers start: 51 outliers final: 24 residues processed: 186 average time/residue: 0.2940 time to fit residues: 93.8755 Evaluate side-chains 159 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 1283 ASP Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1511 GLN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 0.0040 chunk 198 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1559 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23053 Z= 0.256 Angle : 0.652 14.451 31306 Z= 0.335 Chirality : 0.042 0.165 3583 Planarity : 0.005 0.059 4009 Dihedral : 6.443 82.672 3223 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.74 % Allowed : 16.12 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.16), residues: 2908 helix: 1.36 (0.14), residues: 1425 sheet: -1.32 (0.28), residues: 337 loop : -2.75 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.006 0.001 HIS B 676 PHE 0.033 0.002 PHE B1316 TYR 0.020 0.002 TYR B 954 ARG 0.004 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 144 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6514 (m-90) REVERT: A 671 MET cc_start: 0.4463 (tpt) cc_final: 0.4057 (ttt) REVERT: A 734 MET cc_start: 0.8759 (tmm) cc_final: 0.8262 (tmm) REVERT: A 822 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8666 (mp10) REVERT: A 1193 GLU cc_start: 0.6191 (mp0) cc_final: 0.5442 (mp0) REVERT: B 517 TYR cc_start: 0.7364 (m-80) cc_final: 0.6967 (m-80) REVERT: B 803 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 886 MET cc_start: 0.8466 (tmm) cc_final: 0.8248 (tmm) REVERT: B 1475 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9119 (pp) REVERT: C 1 MET cc_start: 0.5371 (tpt) cc_final: 0.4914 (tpt) REVERT: D 143 SER cc_start: 0.8727 (t) cc_final: 0.8439 (p) outliers start: 65 outliers final: 31 residues processed: 198 average time/residue: 0.2914 time to fit residues: 98.5165 Evaluate side-chains 169 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 208 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1133 GLN ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23053 Z= 0.213 Angle : 0.635 13.641 31306 Z= 0.323 Chirality : 0.042 0.405 3583 Planarity : 0.005 0.085 4009 Dihedral : 6.312 83.980 3223 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.12 % Allowed : 17.26 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.16), residues: 2908 helix: 1.51 (0.14), residues: 1423 sheet: -1.24 (0.28), residues: 344 loop : -2.67 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.005 0.001 HIS A 321 PHE 0.016 0.001 PHE A 296 TYR 0.020 0.001 TYR B 608 ARG 0.004 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 145 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6825 (OUTLIER) cc_final: 0.6531 (m-90) REVERT: A 567 LEU cc_start: 0.7913 (pp) cc_final: 0.7226 (tt) REVERT: A 646 ILE cc_start: 0.8465 (pt) cc_final: 0.8138 (tp) REVERT: A 671 MET cc_start: 0.4431 (tpt) cc_final: 0.4142 (ttt) REVERT: A 734 MET cc_start: 0.8717 (tmm) cc_final: 0.8222 (tmm) REVERT: A 822 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: A 1096 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: A 1193 GLU cc_start: 0.6108 (mp0) cc_final: 0.5443 (mp0) REVERT: B 517 TYR cc_start: 0.7355 (m-10) cc_final: 0.6962 (m-80) REVERT: B 541 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6428 (tt) REVERT: B 803 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 886 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8237 (tmm) REVERT: C 1 MET cc_start: 0.5275 (tpt) cc_final: 0.4891 (tpt) REVERT: C 217 TYR cc_start: 0.8819 (m-80) cc_final: 0.8598 (m-80) REVERT: D 143 SER cc_start: 0.8771 (t) cc_final: 0.8475 (p) outliers start: 74 outliers final: 39 residues processed: 209 average time/residue: 0.2986 time to fit residues: 106.2962 Evaluate side-chains 179 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 0.0970 chunk 92 optimal weight: 20.0000 chunk 147 optimal weight: 0.0980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23053 Z= 0.172 Angle : 0.615 13.966 31306 Z= 0.310 Chirality : 0.040 0.204 3583 Planarity : 0.004 0.069 4009 Dihedral : 6.146 85.113 3223 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.87 % Allowed : 18.15 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.16), residues: 2908 helix: 1.70 (0.14), residues: 1425 sheet: -0.98 (0.29), residues: 331 loop : -2.61 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.005 0.001 HIS A 321 PHE 0.034 0.001 PHE B1316 TYR 0.014 0.001 TYR B 608 ARG 0.008 0.000 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 150 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6471 (m-90) REVERT: A 567 LEU cc_start: 0.7797 (pp) cc_final: 0.7115 (tt) REVERT: A 646 ILE cc_start: 0.8390 (pt) cc_final: 0.8146 (tp) REVERT: A 671 MET cc_start: 0.4547 (tpt) cc_final: 0.4114 (ttt) REVERT: A 734 MET cc_start: 0.8662 (tmm) cc_final: 0.8223 (tmm) REVERT: A 822 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: A 1096 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: A 1193 GLU cc_start: 0.6010 (mp0) cc_final: 0.5397 (mp0) REVERT: B 517 TYR cc_start: 0.7443 (m-10) cc_final: 0.7000 (m-80) REVERT: B 541 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6397 (tt) REVERT: B 803 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 886 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8169 (tmm) REVERT: B 1201 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: C 1 MET cc_start: 0.5253 (tpt) cc_final: 0.4985 (tpt) REVERT: C 136 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 217 TYR cc_start: 0.8817 (m-80) cc_final: 0.8612 (m-80) REVERT: D 111 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (m) REVERT: D 143 SER cc_start: 0.8739 (t) cc_final: 0.8422 (p) outliers start: 68 outliers final: 43 residues processed: 208 average time/residue: 0.3036 time to fit residues: 107.6282 Evaluate side-chains 189 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1201 ARG Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1547 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 270 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 279 optimal weight: 0.0020 chunk 174 optimal weight: 7.9990 chunk 170 optimal weight: 0.0050 chunk 129 optimal weight: 8.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23053 Z= 0.151 Angle : 0.601 12.463 31306 Z= 0.300 Chirality : 0.040 0.322 3583 Planarity : 0.004 0.062 4009 Dihedral : 5.985 86.275 3223 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.41 % Allowed : 18.95 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.16), residues: 2908 helix: 1.83 (0.14), residues: 1431 sheet: -0.81 (0.30), residues: 326 loop : -2.60 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1436 HIS 0.005 0.001 HIS A 321 PHE 0.014 0.001 PHE D 150 TYR 0.012 0.001 TYR D 162 ARG 0.005 0.000 ARG A1041 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 157 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.7784 (pp) cc_final: 0.7011 (tt) REVERT: A 646 ILE cc_start: 0.8361 (pt) cc_final: 0.8037 (tp) REVERT: A 671 MET cc_start: 0.4379 (tpt) cc_final: 0.4117 (ttt) REVERT: A 734 MET cc_start: 0.8632 (tmm) cc_final: 0.8273 (tmm) REVERT: A 822 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8607 (mp10) REVERT: A 1038 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 1096 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 1193 GLU cc_start: 0.6021 (mp0) cc_final: 0.5435 (mp0) REVERT: B 517 TYR cc_start: 0.7430 (m-10) cc_final: 0.6985 (m-80) REVERT: B 541 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6377 (tt) REVERT: B 886 MET cc_start: 0.8511 (tmm) cc_final: 0.8155 (tmm) REVERT: C 1 MET cc_start: 0.5043 (tpt) cc_final: 0.4840 (tpt) REVERT: C 136 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 143 SER cc_start: 0.8708 (t) cc_final: 0.8374 (p) outliers start: 57 outliers final: 36 residues processed: 204 average time/residue: 0.2966 time to fit residues: 102.3634 Evaluate side-chains 177 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 54 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 219 optimal weight: 0.0020 chunk 254 optimal weight: 0.0170 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23053 Z= 0.185 Angle : 0.610 15.999 31306 Z= 0.305 Chirality : 0.041 0.321 3583 Planarity : 0.004 0.062 4009 Dihedral : 5.945 86.813 3223 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.79 % Allowed : 19.00 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2908 helix: 1.88 (0.14), residues: 1437 sheet: -0.81 (0.30), residues: 321 loop : -2.56 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 307 HIS 0.005 0.001 HIS A 321 PHE 0.022 0.001 PHE B1316 TYR 0.013 0.001 TYR B 954 ARG 0.003 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 140 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 LEU cc_start: 0.7766 (pp) cc_final: 0.6984 (tt) REVERT: A 646 ILE cc_start: 0.8367 (pt) cc_final: 0.8077 (tp) REVERT: A 671 MET cc_start: 0.4358 (tpt) cc_final: 0.4078 (ttt) REVERT: A 681 MET cc_start: 0.5648 (mmp) cc_final: 0.5445 (tpp) REVERT: A 734 MET cc_start: 0.8627 (tmm) cc_final: 0.8272 (tmm) REVERT: A 822 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: A 1038 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 1084 MET cc_start: 0.7231 (tpp) cc_final: 0.7017 (tpp) REVERT: A 1096 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: A 1193 GLU cc_start: 0.6076 (mp0) cc_final: 0.5545 (mp0) REVERT: B 517 TYR cc_start: 0.7434 (m-10) cc_final: 0.7000 (m-80) REVERT: B 541 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6424 (tt) REVERT: B 886 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8338 (tmm) REVERT: B 1201 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8137 (ttm-80) REVERT: C 136 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 143 SER cc_start: 0.8711 (t) cc_final: 0.8400 (p) outliers start: 66 outliers final: 48 residues processed: 195 average time/residue: 0.3075 time to fit residues: 100.8846 Evaluate side-chains 189 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 136 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1201 ARG Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1547 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN B 588 GLN B 777 ASN B1356 ASN ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 23053 Z= 0.470 Angle : 0.803 16.072 31306 Z= 0.409 Chirality : 0.047 0.342 3583 Planarity : 0.006 0.063 4009 Dihedral : 6.567 85.500 3223 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.21 % Favored : 89.75 % Rotamer: Outliers : 3.04 % Allowed : 19.21 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.15), residues: 2908 helix: 1.20 (0.14), residues: 1439 sheet: -1.34 (0.27), residues: 359 loop : -2.71 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 49 HIS 0.012 0.002 HIS C 184 PHE 0.018 0.002 PHE B1479 TYR 0.024 0.002 TYR B 972 ARG 0.007 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 132 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8084 (ptp90) REVERT: A 646 ILE cc_start: 0.8439 (pt) cc_final: 0.8158 (tp) REVERT: A 671 MET cc_start: 0.4730 (tpt) cc_final: 0.4435 (ttt) REVERT: A 734 MET cc_start: 0.8706 (tmm) cc_final: 0.8258 (tmm) REVERT: A 1096 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: A 1193 GLU cc_start: 0.6193 (mp0) cc_final: 0.5665 (mp0) REVERT: B 1201 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8080 (ttm-80) REVERT: D 143 SER cc_start: 0.8804 (t) cc_final: 0.8541 (p) outliers start: 72 outliers final: 53 residues processed: 191 average time/residue: 0.3168 time to fit residues: 100.6403 Evaluate side-chains 182 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 900 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1201 ARG Chi-restraints excluded: chain B residue 1283 ASP Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1547 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 275 optimal weight: 0.9980 chunk 168 optimal weight: 0.0770 chunk 130 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 177 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 777 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23053 Z= 0.168 Angle : 0.659 15.602 31306 Z= 0.327 Chirality : 0.042 0.377 3583 Planarity : 0.004 0.059 4009 Dihedral : 6.138 87.634 3223 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.11 % Allowed : 19.92 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.16), residues: 2908 helix: 1.73 (0.14), residues: 1430 sheet: -1.09 (0.28), residues: 349 loop : -2.63 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1436 HIS 0.006 0.001 HIS A 321 PHE 0.016 0.001 PHE D 150 TYR 0.045 0.001 TYR B1510 ARG 0.006 0.000 ARG B1507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ILE cc_start: 0.8339 (pt) cc_final: 0.8039 (tp) REVERT: A 671 MET cc_start: 0.4410 (tpt) cc_final: 0.4096 (ttt) REVERT: A 734 MET cc_start: 0.8574 (tmm) cc_final: 0.8294 (tmm) REVERT: A 822 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: A 1038 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 1084 MET cc_start: 0.7267 (tpp) cc_final: 0.7020 (tpp) REVERT: A 1096 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 1193 GLU cc_start: 0.6019 (mp0) cc_final: 0.5537 (mp0) REVERT: B 546 MET cc_start: 0.8677 (ppp) cc_final: 0.8351 (ppp) REVERT: B 1201 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: C 51 ASP cc_start: 0.7577 (p0) cc_final: 0.7178 (p0) REVERT: D 143 SER cc_start: 0.8710 (t) cc_final: 0.8406 (p) outliers start: 50 outliers final: 40 residues processed: 181 average time/residue: 0.2846 time to fit residues: 87.7562 Evaluate side-chains 178 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1201 ARG Chi-restraints excluded: chain B residue 1313 ASP Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1547 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067980 restraints weight = 90785.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069716 restraints weight = 47749.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070903 restraints weight = 31543.081| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23053 Z= 0.187 Angle : 0.638 15.325 31306 Z= 0.316 Chirality : 0.041 0.357 3583 Planarity : 0.004 0.061 4009 Dihedral : 6.018 87.421 3223 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.32 % Allowed : 20.14 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2908 helix: 1.80 (0.14), residues: 1442 sheet: -1.09 (0.28), residues: 351 loop : -2.64 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.007 0.001 HIS A 321 PHE 0.013 0.001 PHE D 150 TYR 0.017 0.001 TYR B1510 ARG 0.004 0.000 ARG A 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.02 seconds wall clock time: 72 minutes 16.37 seconds (4336.37 seconds total)