Starting phenix.real_space_refine on Thu Apr 11 22:35:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z11_11026/04_2024/6z11_11026.pdb" } resolution = 3.36 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= 0.002 sd= 0.024 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 87 5.16 5 C 14991 2.51 5 N 4254 2.21 5 O 4613 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 ARG 40": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C ARG 686": "NH1" <-> "NH2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ASP 763": "OD1" <-> "OD2" Residue "C ARG 788": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C GLU 847": "OE1" <-> "OE2" Residue "C GLU 851": "OE1" <-> "OE2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 916": "NH1" <-> "NH2" Residue "C ASP 938": "OD1" <-> "OD2" Residue "C ARG 987": "NH1" <-> "NH2" Residue "C ASP 1029": "OD1" <-> "OD2" Residue "C PHE 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1058": "NH1" <-> "NH2" Residue "C GLU 1061": "OE1" <-> "OE2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 246": "OD1" <-> "OD2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 427": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 630": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 725": "NH1" <-> "NH2" Residue "D ARG 833": "NH1" <-> "NH2" Residue "D ARG 840": "NH1" <-> "NH2" Residue "D ARG 886": "NH1" <-> "NH2" Residue "D ARG 903": "NH1" <-> "NH2" Residue "D ARG 962": "NH1" <-> "NH2" Residue "D ARG 980": "NH1" <-> "NH2" Residue "D ARG 1012": "NH1" <-> "NH2" Residue "D PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1031": "NH1" <-> "NH2" Residue "D GLU 1034": "OE1" <-> "OE2" Residue "D ARG 1042": "NH1" <-> "NH2" Residue "D ASP 1049": "OD1" <-> "OD2" Residue "D ASP 1070": "OD1" <-> "OD2" Residue "D ARG 1084": "NH1" <-> "NH2" Residue "D ARG 1086": "NH1" <-> "NH2" Residue "D ARG 1129": "NH1" <-> "NH2" Residue "D PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1193": "NH1" <-> "NH2" Residue "D ARG 1232": "NH1" <-> "NH2" Residue "D ASP 1236": "OD1" <-> "OD2" Residue "D ARG 1269": "NH1" <-> "NH2" Residue "D ARG 1280": "NH1" <-> "NH2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 127": "NH1" <-> "NH2" Residue "H ASP 138": "OD1" <-> "OD2" Residue "H ARG 458": "NH1" <-> "NH2" Residue "H ARG 461": "NH1" <-> "NH2" Residue "H ASP 476": "OD1" <-> "OD2" Residue "H ARG 477": "NH1" <-> "NH2" Residue "H ASP 479": "OD1" <-> "OD2" Residue "H ASP 500": "OD1" <-> "OD2" Residue "H ARG 501": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1700 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Chain: "B" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1783 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Chain: "C" Number of atoms: 8433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8433 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 9826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9826 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1197} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "H" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1563 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18925 SG CYS D 890 35.486 59.610 77.607 1.00 25.70 S ATOM 19487 SG CYS D 967 38.115 62.172 78.213 1.00 22.34 S ATOM 19529 SG CYS D 974 36.383 60.503 81.055 1.00 21.46 S ATOM 19548 SG CYS D 977 38.738 58.556 79.254 1.00 20.41 S ATOM 12390 SG CYS D 60 41.523 123.724 95.786 1.00 69.43 S ATOM 12408 SG CYS D 62 43.027 127.404 96.225 1.00 73.10 S ATOM 12517 SG CYS D 75 40.569 126.973 93.957 1.00 69.31 S ATOM 12543 SG CYS D 78 43.892 125.420 93.141 1.00 71.22 S Time building chain proxies: 12.83, per 1000 atoms: 0.54 Number of scatterers: 23948 At special positions: 0 Unit cell: (130.483, 145.442, 173.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 87 16.00 Mg 1 11.99 O 4613 8.00 N 4254 7.00 C 14991 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: 9.17 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 41 sheets defined 35.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.534A pdb=" N LYS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.779A pdb=" N SER A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.919A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.677A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.912A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.847A pdb=" N VAL C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 254 removed outlier: 4.231A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.544A pdb=" N LYS C 310 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.706A pdb=" N GLU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 396 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 411 through 424 removed outlier: 3.537A pdb=" N VAL C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.658A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.962A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 725 " --> pdb=" O TYR C 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 773 removed outlier: 4.382A pdb=" N LEU C 772 " --> pdb=" O SER C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 909 through 913 removed outlier: 4.092A pdb=" N GLY C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 913 " --> pdb=" O THR C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 913' Processing helix chain 'C' and resid 919 through 933 removed outlier: 3.631A pdb=" N LEU C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1050 through 1054 Processing helix chain 'C' and resid 1060 through 1069 removed outlier: 3.624A pdb=" N CYS C1064 " --> pdb=" O GLY C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1082 Processing helix chain 'C' and resid 1088 through 1100 Processing helix chain 'C' and resid 1109 through 1120 removed outlier: 3.530A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1123 No H-bonds generated for 'chain 'C' and resid 1121 through 1123' Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.833A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.026A pdb=" N LEU D 39 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.706A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 123 through 130 removed outlier: 4.209A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 185 removed outlier: 4.157A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.041A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 260 through 268 removed outlier: 4.420A pdb=" N GLU D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 288 through 302 removed outlier: 3.642A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.938A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 382 removed outlier: 3.986A pdb=" N ALA D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.870A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.799A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.808A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.526A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 removed outlier: 3.755A pdb=" N VAL D 670 " --> pdb=" O THR D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 724 removed outlier: 4.043A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN D 710 " --> pdb=" O ILE D 706 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 removed outlier: 4.015A pdb=" N ILE D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.969A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 880 removed outlier: 3.968A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.511A pdb=" N SER D 918 " --> pdb=" O HIS D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 995 through 1004 removed outlier: 3.563A pdb=" N ALA D 999 " --> pdb=" O GLY D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 removed outlier: 3.857A pdb=" N LEU D1009 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1036 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1130 through 1145 Processing helix chain 'D' and resid 1155 through 1160 removed outlier: 3.700A pdb=" N ARG D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1163 No H-bonds generated for 'chain 'D' and resid 1161 through 1163' Processing helix chain 'D' and resid 1184 through 1190 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.587A pdb=" N ALA D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1240 removed outlier: 3.617A pdb=" N VAL D1233 " --> pdb=" O GLU D1229 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN D1240 " --> pdb=" O ASP D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.545A pdb=" N THR E 33 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 46 through 67 removed outlier: 4.260A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 4 through 41 removed outlier: 3.706A pdb=" N GLU H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 65 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.907A pdb=" N ARG H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 480 removed outlier: 3.822A pdb=" N LEU H 480 " --> pdb=" O ARG H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 26 removed outlier: 5.942A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 196 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL A 22 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.112A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 145 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.112A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.646A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 181 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.579A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.612A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.685A pdb=" N ASN C 132 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.621A pdb=" N ARG C 102 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 182 removed outlier: 3.709A pdb=" N LEU C 190 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.451A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC2, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.873A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 617 through 618 Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.732A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 643 removed outlier: 5.568A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 699 through 700 removed outlier: 3.722A pdb=" N GLU C 703 " --> pdb=" O GLN C 700 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 883 through 885 removed outlier: 4.559A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 714 " --> pdb=" O THR C1015 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 883 through 885 Processing sheet with id=AC9, first strand: chain 'C' and resid 740 through 750 removed outlier: 3.665A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'C' and resid 792 through 794 removed outlier: 4.022A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 3.529A pdb=" N GLY D 426 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 517 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1127 through 1128 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 6.330A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 328 through 330 removed outlier: 3.865A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 898 Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 903 Processing sheet with id=AE1, first strand: chain 'D' and resid 1076 through 1077 removed outlier: 3.603A pdb=" N PHE D1063 " --> pdb=" O LEU D1081 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D1081 " --> pdb=" O PHE D1063 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1076 through 1077 Processing sheet with id=AE3, first strand: chain 'D' and resid 1182 through 1183 removed outlier: 3.502A pdb=" N THR D1167 " --> pdb=" O ARG D1205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.803A pdb=" N GLN D1272 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 104 " --> pdb=" O GLN D1272 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D1274 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 98 through 103 removed outlier: 7.186A pdb=" N ASP H 92 " --> pdb=" O PRO H 99 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU H 88 " --> pdb=" O ASP H 103 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 87 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS H 71 " --> pdb=" O ARG H 87 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2481 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: 9.85 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8291 1.34 - 1.46: 4551 1.46 - 1.58: 11342 1.58 - 1.70: 0 1.70 - 1.81: 155 Bond restraints: 24339 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.48e+00 bond pdb=" CD ARG D 980 " pdb=" NE ARG D 980 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.40e-02 5.10e+03 1.72e+00 bond pdb=" CB VAL C 930 " pdb=" CG1 VAL C 930 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" N VAL D 431 " pdb=" CA VAL D 431 " ideal model delta sigma weight residual 1.459 1.443 0.016 1.25e-02 6.40e+03 1.56e+00 ... (remaining 24334 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.33: 560 105.33 - 112.51: 12417 112.51 - 119.68: 8219 119.68 - 126.85: 11489 126.85 - 134.02: 263 Bond angle restraints: 32948 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.42 109.17 4.25 1.17e+00 7.31e-01 1.32e+01 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 119.10 -5.20 1.80e+00 3.09e-01 8.36e+00 angle pdb=" C GLU C 723 " pdb=" N ASP C 724 " pdb=" CA ASP C 724 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.99e+00 angle pdb=" C GLY E 83 " pdb=" N LEU E 84 " pdb=" CA LEU E 84 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.89e+00 angle pdb=" C ILE E 52 " pdb=" N TYR E 53 " pdb=" CA TYR E 53 " ideal model delta sigma weight residual 120.60 124.58 -3.98 1.60e+00 3.91e-01 6.18e+00 ... (remaining 32943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13331 17.74 - 35.48: 1355 35.48 - 53.21: 197 53.21 - 70.95: 39 70.95 - 88.69: 11 Dihedral angle restraints: 14933 sinusoidal: 6123 harmonic: 8810 Sorted by residual: dihedral pdb=" CA GLY E 83 " pdb=" C GLY E 83 " pdb=" N LEU E 84 " pdb=" CA LEU E 84 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA THR C 404 " pdb=" C THR C 404 " pdb=" N PRO C 405 " pdb=" CA PRO C 405 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR D 130 " pdb=" C TYR D 130 " pdb=" N PHE D 131 " pdb=" CA PHE D 131 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 14930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2192 0.031 - 0.062: 1037 0.062 - 0.093: 349 0.093 - 0.124: 152 0.124 - 0.155: 15 Chirality restraints: 3745 Sorted by residual: chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA VAL C 193 " pdb=" N VAL C 193 " pdb=" C VAL C 193 " pdb=" CB VAL C 193 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE D 34 " pdb=" N ILE D 34 " pdb=" C ILE D 34 " pdb=" CB ILE D 34 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 3742 not shown) Planarity restraints: 4357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 404 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO C 405 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 545 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO D 546 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 546 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 546 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 110 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 111 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 111 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 111 " 0.029 5.00e-02 4.00e+02 ... (remaining 4354 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 148 2.50 - 3.10: 19032 3.10 - 3.70: 33411 3.70 - 4.30: 50143 4.30 - 4.90: 85328 Nonbonded interactions: 188062 Sorted by model distance: nonbonded pdb=" OD1 ASP D 539 " pdb=" OD1 ASP H 483 " model vdw 1.906 3.040 nonbonded pdb=" OD2 ASP H 483 " pdb="MG MG D2003 " model vdw 1.929 2.170 nonbonded pdb=" NH2 ARG E 57 " pdb=" O GLY E 77 " model vdw 2.071 2.520 nonbonded pdb=" NH1 ARG D 875 " pdb=" OG1 THR D1212 " model vdw 2.078 2.520 nonbonded pdb=" OG SER C 173 " pdb=" OH TYR C 177 " model vdw 2.080 2.440 ... (remaining 188057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 224) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.780 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 69.600 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 87.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24339 Z= 0.355 Angle : 0.612 5.962 32948 Z= 0.342 Chirality : 0.042 0.155 3745 Planarity : 0.004 0.056 4357 Dihedral : 14.183 88.688 9261 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -5.38 (0.11), residues: 3053 helix: -2.89 (0.12), residues: 1001 sheet: -3.14 (0.23), residues: 346 loop : -4.29 (0.11), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 104 HIS 0.007 0.001 HIS D 505 PHE 0.012 0.001 PHE D 920 TYR 0.032 0.001 TYR E 53 ARG 0.006 0.001 ARG C1090 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.4934 time to fit residues: 220.7132 Evaluate side-chains 180 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 749 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN C 880 HIS ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 35 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 766 HIS ** D1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24339 Z= 0.212 Angle : 0.619 11.310 32948 Z= 0.320 Chirality : 0.044 0.229 3745 Planarity : 0.005 0.051 4357 Dihedral : 4.857 37.501 3374 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.20 % Allowed : 8.71 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.14), residues: 3053 helix: -0.70 (0.16), residues: 997 sheet: -2.34 (0.25), residues: 347 loop : -3.20 (0.13), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 58 HIS 0.016 0.001 HIS H 130 PHE 0.017 0.001 PHE B 219 TYR 0.018 0.001 TYR E 53 ARG 0.008 0.001 ARG D 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 GLN cc_start: 0.6772 (pp30) cc_final: 0.6408 (pp30) REVERT: C 319 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6325 (mp) REVERT: C 570 MET cc_start: 0.7264 (ttt) cc_final: 0.7062 (ttt) outliers start: 31 outliers final: 14 residues processed: 226 average time/residue: 0.3980 time to fit residues: 139.4022 Evaluate side-chains 181 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 1233 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 479 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 277 optimal weight: 0.1980 chunk 299 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 HIS C 512 ASN ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 932 ASN ** D1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24339 Z= 0.156 Angle : 0.548 9.138 32948 Z= 0.281 Chirality : 0.042 0.249 3745 Planarity : 0.004 0.046 4357 Dihedral : 4.433 42.705 3374 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.39 % Allowed : 11.46 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 3053 helix: 0.26 (0.17), residues: 1015 sheet: -1.62 (0.26), residues: 358 loop : -2.61 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 58 HIS 0.003 0.001 HIS H 130 PHE 0.015 0.001 PHE C 130 TYR 0.015 0.001 TYR E 53 ARG 0.006 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 2.611 Fit side-chains revert: symmetry clash REVERT: C 319 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6158 (mp) REVERT: D 205 MET cc_start: 0.4661 (mmm) cc_final: 0.4258 (mmt) outliers start: 36 outliers final: 15 residues processed: 233 average time/residue: 0.4109 time to fit residues: 146.4434 Evaluate side-chains 177 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain H residue 479 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 686 GLN D 766 HIS D1132 GLN ** D1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 24339 Z= 0.575 Angle : 0.790 13.575 32948 Z= 0.405 Chirality : 0.050 0.200 3745 Planarity : 0.006 0.056 4357 Dihedral : 5.200 45.801 3374 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.83 % Allowed : 13.32 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3053 helix: -0.08 (0.16), residues: 1028 sheet: -1.61 (0.27), residues: 360 loop : -2.48 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 58 HIS 0.007 0.001 HIS B 231 PHE 0.021 0.002 PHE C1002 TYR 0.033 0.002 TYR E 53 ARG 0.009 0.001 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.7432 (t0) cc_final: 0.7231 (t0) REVERT: C 96 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6153 (tp) outliers start: 73 outliers final: 43 residues processed: 234 average time/residue: 0.4127 time to fit residues: 151.2671 Evaluate side-chains 201 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 211 ARG Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 1187 PHE Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24339 Z= 0.166 Angle : 0.552 10.156 32948 Z= 0.283 Chirality : 0.042 0.169 3745 Planarity : 0.004 0.048 4357 Dihedral : 4.627 54.288 3374 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.40 % Allowed : 15.22 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.54 (0.15), residues: 3053 helix: 0.60 (0.17), residues: 1015 sheet: -1.38 (0.28), residues: 345 loop : -2.05 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 58 HIS 0.003 0.001 HIS B 124 PHE 0.013 0.001 PHE B 219 TYR 0.015 0.001 TYR D 241 ARG 0.009 0.000 ARG D1192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 173 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.7264 (t0) cc_final: 0.7048 (t0) REVERT: C 319 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6062 (mp) REVERT: H 481 MET cc_start: 0.4146 (mtt) cc_final: 0.3798 (mtt) outliers start: 62 outliers final: 36 residues processed: 226 average time/residue: 0.3894 time to fit residues: 138.4783 Evaluate side-chains 196 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1271 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24339 Z= 0.231 Angle : 0.567 10.764 32948 Z= 0.288 Chirality : 0.042 0.163 3745 Planarity : 0.004 0.045 4357 Dihedral : 4.474 54.926 3374 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.44 % Allowed : 16.11 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.33 (0.15), residues: 3053 helix: 0.71 (0.17), residues: 1023 sheet: -1.29 (0.27), residues: 366 loop : -1.89 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 58 HIS 0.003 0.001 HIS D 505 PHE 0.013 0.001 PHE B 219 TYR 0.016 0.001 TYR E 53 ARG 0.009 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 168 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.7375 (t0) cc_final: 0.7156 (t0) REVERT: C 133 ASN cc_start: 0.6963 (p0) cc_final: 0.6677 (p0) REVERT: C 319 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6187 (mp) REVERT: C 717 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.8717 (t60) REVERT: D 143 MET cc_start: 0.5493 (ptm) cc_final: 0.5038 (ptm) REVERT: D 223 TRP cc_start: 0.4492 (t-100) cc_final: 0.2321 (t60) REVERT: H 481 MET cc_start: 0.4058 (mtt) cc_final: 0.3709 (mtt) outliers start: 63 outliers final: 51 residues processed: 218 average time/residue: 0.3850 time to fit residues: 133.1821 Evaluate side-chains 211 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 158 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1187 PHE Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1271 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 293 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24339 Z= 0.164 Angle : 0.535 11.771 32948 Z= 0.272 Chirality : 0.041 0.171 3745 Planarity : 0.004 0.083 4357 Dihedral : 4.358 57.160 3374 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.36 % Allowed : 16.77 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.11 (0.15), residues: 3053 helix: 0.89 (0.17), residues: 1019 sheet: -1.12 (0.28), residues: 363 loop : -1.75 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 PHE 0.011 0.001 PHE B 219 TYR 0.016 0.001 TYR C 305 ARG 0.004 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 165 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.7392 (t0) cc_final: 0.7135 (t0) REVERT: C 133 ASN cc_start: 0.6986 (p0) cc_final: 0.6711 (p0) REVERT: C 319 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6190 (mp) REVERT: C 717 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8536 (t60) REVERT: D 223 TRP cc_start: 0.4443 (t-100) cc_final: 0.2311 (t60) REVERT: H 481 MET cc_start: 0.4074 (mtt) cc_final: 0.3710 (mtt) outliers start: 61 outliers final: 46 residues processed: 215 average time/residue: 0.3850 time to fit residues: 131.1302 Evaluate side-chains 206 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 0.0970 chunk 27 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24339 Z= 0.209 Angle : 0.547 11.933 32948 Z= 0.279 Chirality : 0.042 0.160 3745 Planarity : 0.004 0.071 4357 Dihedral : 4.334 57.278 3374 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.40 % Allowed : 17.04 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -1.03 (0.15), residues: 3053 helix: 0.94 (0.17), residues: 1022 sheet: -1.14 (0.27), residues: 374 loop : -1.68 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 PHE 0.011 0.001 PHE B 219 TYR 0.014 0.001 TYR C 305 ARG 0.003 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 158 time to evaluate : 3.116 Fit side-chains revert: symmetry clash REVERT: C 319 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6202 (mp) REVERT: C 717 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8645 (t60) REVERT: D 223 TRP cc_start: 0.4314 (t-100) cc_final: 0.2231 (t60) REVERT: H 481 MET cc_start: 0.4101 (mtt) cc_final: 0.3772 (mtt) outliers start: 62 outliers final: 53 residues processed: 208 average time/residue: 0.3779 time to fit residues: 125.6081 Evaluate side-chains 210 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 155 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1271 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 479 ASP Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 247 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24339 Z= 0.188 Angle : 0.539 12.584 32948 Z= 0.275 Chirality : 0.042 0.159 3745 Planarity : 0.004 0.067 4357 Dihedral : 4.289 57.961 3374 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.36 % Allowed : 17.39 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.92 (0.15), residues: 3053 helix: 1.02 (0.17), residues: 1019 sheet: -1.13 (0.27), residues: 384 loop : -1.58 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 PHE 0.010 0.001 PHE B 219 TYR 0.014 0.001 TYR C 305 ARG 0.003 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 163 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: C 319 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6168 (mp) REVERT: C 717 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.8558 (t60) REVERT: D 215 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.4026 (pt0) REVERT: D 223 TRP cc_start: 0.4261 (t-100) cc_final: 0.2206 (t60) REVERT: H 481 MET cc_start: 0.4111 (mtt) cc_final: 0.3785 (mtt) outliers start: 61 outliers final: 53 residues processed: 214 average time/residue: 0.3949 time to fit residues: 134.0527 Evaluate side-chains 211 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 201 optimal weight: 0.0980 chunk 303 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24339 Z= 0.210 Angle : 0.550 12.465 32948 Z= 0.280 Chirality : 0.042 0.160 3745 Planarity : 0.004 0.063 4357 Dihedral : 4.298 57.769 3374 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.25 % Allowed : 17.78 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.86 (0.15), residues: 3053 helix: 1.05 (0.17), residues: 1024 sheet: -1.05 (0.27), residues: 374 loop : -1.55 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 PHE 0.012 0.001 PHE C 292 TYR 0.015 0.001 TYR E 53 ARG 0.006 0.000 ARG C 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 319 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6167 (mp) REVERT: C 717 TRP cc_start: 0.9052 (OUTLIER) cc_final: 0.8658 (t60) REVERT: D 215 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.4061 (pt0) REVERT: H 481 MET cc_start: 0.4115 (mtt) cc_final: 0.3791 (mtt) outliers start: 58 outliers final: 54 residues processed: 212 average time/residue: 0.3887 time to fit residues: 129.9583 Evaluate side-chains 217 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 493 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 242 optimal weight: 0.0870 chunk 101 optimal weight: 0.0970 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.083527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.065870 restraints weight = 72193.305| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.73 r_work: 0.3090 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24339 Z= 0.181 Angle : 0.536 10.369 32948 Z= 0.274 Chirality : 0.042 0.159 3745 Planarity : 0.004 0.062 4357 Dihedral : 4.252 58.479 3374 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.40 % Allowed : 17.85 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: -0.76 (0.15), residues: 3053 helix: 1.13 (0.17), residues: 1021 sheet: -1.03 (0.27), residues: 374 loop : -1.48 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 PHE 0.010 0.001 PHE C 292 TYR 0.014 0.001 TYR E 53 ARG 0.003 0.000 ARG D 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.02 seconds wall clock time: 88 minutes 17.92 seconds (5297.92 seconds total)