Starting phenix.real_space_refine on Sun Sep 29 13:23:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uro_20861/09_2024/6uro_20861.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 3 6.06 5 P 8 5.49 5 S 135 5.16 5 C 14319 2.51 5 N 3853 2.21 5 O 4083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22401 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9498 Classifications: {'peptide': 1199} Link IDs: {'PTRANS': 66, 'TRANS': 1132} Chain breaks: 10 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 15, 'TRANS': 362} Chain: "C" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 172 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 1} Chain: "E" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4382 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 16, 'TRANS': 510} Chain breaks: 1 Chain: "F" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4382 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 16, 'TRANS': 510} Chain breaks: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12855 SG CYS C 41 68.174 61.972 19.751 1.00 39.96 S ATOM 12954 SG CYS C 55 71.000 59.886 22.804 1.00 39.96 S ATOM 13056 SG CYS C 68 52.178 51.192 23.941 1.00 30.00 S ATOM 13171 SG CYS C 82 55.511 50.824 21.577 1.00 52.97 S ATOM 13292 SG CYS C 96 36.481 48.944 23.117 1.00 39.93 S ATOM 13410 SG CYS C 110 36.082 52.254 24.468 1.00 37.40 S Time building chain proxies: 12.47, per 1000 atoms: 0.56 Number of scatterers: 22401 At special positions: 0 Unit cell: (101.65, 161.57, 208.65, 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 3 29.99 S 135 16.00 P 8 15.00 O 4083 8.00 N 3853 7.00 C 14319 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 - 3.00 Amino acid : True - 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: 5.98 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 82 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 37 sheets defined 36.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.709A pdb=" N ARG A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.517A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.587A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A1369 " --> pdb=" O ALA A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1411 through 1421 removed outlier: 3.651A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 removed outlier: 3.856A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.995A pdb=" N VAL A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.715A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.827A pdb=" N TYR B 89 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.640A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 removed outlier: 3.508A pdb=" N VAL C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 47 removed outlier: 3.986A pdb=" N LEU C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.591A pdb=" N GLN C 81 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS C 82 " --> pdb=" O GLY C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'E' and resid 22 through 28 removed outlier: 3.792A pdb=" N GLU E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 41 removed outlier: 3.606A pdb=" N LEU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.505A pdb=" N ARG E 51 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 59 " --> pdb=" O GLU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 4.118A pdb=" N TYR E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 92 removed outlier: 3.611A pdb=" N GLU E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 92 " --> pdb=" O PHE E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 117 through 133 removed outlier: 3.688A pdb=" N ALA E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS E 132 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.798A pdb=" N TYR E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 176 removed outlier: 3.757A pdb=" N VAL E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.840A pdb=" N LYS E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 209 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 223 Processing helix chain 'E' and resid 223 through 228 removed outlier: 3.715A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 261 removed outlier: 3.598A pdb=" N MET E 251 " --> pdb=" O GLN E 247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.757A pdb=" N ARG E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 311 removed outlier: 3.626A pdb=" N TRP E 294 " --> pdb=" O HIS E 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR E 300 " --> pdb=" O GLU E 296 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 310 " --> pdb=" O LYS E 306 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 334 removed outlier: 3.537A pdb=" N ILE E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 353 removed outlier: 3.594A pdb=" N GLU E 350 " --> pdb=" O TYR E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 368 removed outlier: 3.513A pdb=" N VAL E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 390 removed outlier: 4.195A pdb=" N VAL E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 387 " --> pdb=" O LYS E 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 403 removed outlier: 3.548A pdb=" N ILE E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 424 removed outlier: 3.520A pdb=" N VAL E 413 " --> pdb=" O HIS E 409 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 416 " --> pdb=" O TYR E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 440 removed outlier: 3.633A pdb=" N PHE E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS E 439 " --> pdb=" O LEU E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 455 removed outlier: 3.723A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR E 453 " --> pdb=" O ALA E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 471 Processing helix chain 'E' and resid 481 through 495 removed outlier: 3.510A pdb=" N LEU E 489 " --> pdb=" O TRP E 485 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 512 removed outlier: 3.634A pdb=" N VAL E 504 " --> pdb=" O SER E 500 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 506 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 509 " --> pdb=" O GLU E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.813A pdb=" N GLU E 517 " --> pdb=" O LYS E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 529 removed outlier: 3.565A pdb=" N VAL E 525 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR E 528 " --> pdb=" O LEU E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 545 removed outlier: 4.107A pdb=" N ALA E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 545 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 28 removed outlier: 3.792A pdb=" N GLU F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.605A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.505A pdb=" N ARG F 51 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 78 removed outlier: 4.118A pdb=" N TYR F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 removed outlier: 3.612A pdb=" N GLU F 85 " --> pdb=" O TYR F 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 86 " --> pdb=" O ASP F 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 92 " --> pdb=" O PHE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 112 Processing helix chain 'F' and resid 113 through 115 No H-bonds generated for 'chain 'F' and resid 113 through 115' Processing helix chain 'F' and resid 117 through 133 removed outlier: 3.688A pdb=" N ALA F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS F 132 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.799A pdb=" N TYR F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 176 removed outlier: 3.757A pdb=" N VAL F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 198 Processing helix chain 'F' and resid 198 through 209 removed outlier: 3.840A pdb=" N LYS F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG F 209 " --> pdb=" O MET F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.714A pdb=" N MET F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 261 removed outlier: 3.599A pdb=" N MET F 251 " --> pdb=" O GLN F 247 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 259 " --> pdb=" O TYR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 287 removed outlier: 3.757A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 286 " --> pdb=" O GLN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 311 removed outlier: 3.626A pdb=" N TRP F 294 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR F 300 " --> pdb=" O GLU F 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 310 " --> pdb=" O LYS F 306 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 311 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.535A pdb=" N ILE F 332 " --> pdb=" O TYR F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 353 removed outlier: 3.593A pdb=" N GLU F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 368 removed outlier: 3.513A pdb=" N VAL F 359 " --> pdb=" O LYS F 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS F 360 " --> pdb=" O TYR F 356 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 390 removed outlier: 4.195A pdb=" N VAL F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG F 387 " --> pdb=" O LYS F 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 403 removed outlier: 3.549A pdb=" N ILE F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 424 removed outlier: 3.520A pdb=" N VAL F 413 " --> pdb=" O HIS F 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA F 416 " --> pdb=" O TYR F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 440 removed outlier: 3.633A pdb=" N PHE F 433 " --> pdb=" O ALA F 429 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 439 " --> pdb=" O LEU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 455 removed outlier: 3.723A pdb=" N ALA F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR F 453 " --> pdb=" O ALA F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 471 Processing helix chain 'F' and resid 481 through 495 removed outlier: 3.510A pdb=" N LEU F 489 " --> pdb=" O TRP F 485 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 490 " --> pdb=" O ALA F 486 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN F 494 " --> pdb=" O ALA F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 512 removed outlier: 3.634A pdb=" N VAL F 504 " --> pdb=" O SER F 500 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS F 506 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 509 " --> pdb=" O GLU F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 517 removed outlier: 3.841A pdb=" N GLU F 517 " --> pdb=" O LYS F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 529 removed outlier: 3.564A pdb=" N VAL F 525 " --> pdb=" O THR F 521 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 527 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR F 528 " --> pdb=" O LEU F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 545 removed outlier: 4.108A pdb=" N ALA F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY F 545 " --> pdb=" O LEU F 541 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1348 through 1350 removed outlier: 7.258A pdb=" N ALA A 3 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 4.223A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.521A pdb=" N SER A 80 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.716A pdb=" N ARG A 140 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.856A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.095A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.558A pdb=" N ALA A 359 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 329 removed outlier: 4.133A pdb=" N ALA A 366 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 346 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS A 364 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376 removed outlier: 6.927A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 528 removed outlier: 6.911A pdb=" N ILE A 998 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR A 526 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 996 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 4.076A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 578 " --> pdb=" O ASP A 534 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 538 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 577 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.794A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 620 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 627 " --> pdb=" O GLN A 620 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 626 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 637 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 628 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 651 removed outlier: 3.726A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 701 removed outlier: 3.866A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 699 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 854 removed outlier: 3.503A pdb=" N GLU A 848 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 877 through 878 removed outlier: 3.528A pdb=" N PHE A 877 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.793A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1027 through 1028 Processing sheet with id=AC2, first strand: chain 'A' and resid 1037 through 1043 removed outlier: 3.505A pdb=" N SER A1075 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1046 through 1050 Processing sheet with id=AC4, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.665A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1121 " --> pdb=" O MET A1142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A1139 " --> pdb=" O LYS A1166 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1166 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1144 through 1146 removed outlier: 3.658A pdb=" N LYS A1159 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 4.132A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.569A pdb=" N SER A1232 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU A1243 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 4.299A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 4.299A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1297 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1312 through 1315 removed outlier: 3.550A pdb=" N PHE A1338 " --> pdb=" O GLY A1346 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 112 removed outlier: 6.714A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.499A pdb=" N GLY B 137 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AD5, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.566A pdb=" N LYS B 186 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 180 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 209 through 210 removed outlier: 3.777A pdb=" N VAL B 226 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 247 through 252 removed outlier: 3.969A pdb=" N CYS B 249 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 270 through 273 removed outlier: 3.712A pdb=" N ALA B 282 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.865A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.749A pdb=" N PHE B 347 " --> pdb=" O TRP B 359 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.85 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4003 1.32 - 1.45: 6042 1.45 - 1.57: 12660 1.57 - 1.70: 15 1.70 - 1.82: 221 Bond restraints: 22941 Sorted by residual: bond pdb=" CG GLN B 73 " pdb=" CD GLN B 73 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB VAL B 111 " pdb=" CG2 VAL B 111 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" N ALA A1250 " pdb=" CA ALA A1250 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.21e+00 bond pdb=" CG LEU B 381 " pdb=" CD2 LEU B 381 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.06e+00 bond pdb=" CB ILE A 945 " pdb=" CG2 ILE A 945 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 ... (remaining 22936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30066 2.61 - 5.21: 865 5.21 - 7.82: 100 7.82 - 10.42: 20 10.42 - 13.03: 3 Bond angle restraints: 31054 Sorted by residual: angle pdb=" N LEU B 386 " pdb=" CA LEU B 386 " pdb=" C LEU B 386 " ideal model delta sigma weight residual 109.96 98.27 11.69 1.50e+00 4.44e-01 6.07e+01 angle pdb=" N ILE A 330 " pdb=" CA ILE A 330 " pdb=" C ILE A 330 " ideal model delta sigma weight residual 110.21 102.15 8.06 1.13e+00 7.83e-01 5.09e+01 angle pdb=" N LEU A 392 " pdb=" CA LEU A 392 " pdb=" C LEU A 392 " ideal model delta sigma weight residual 109.85 120.49 -10.64 1.58e+00 4.01e-01 4.53e+01 angle pdb=" N LEU B 99 " pdb=" CA LEU B 99 " pdb=" C LEU B 99 " ideal model delta sigma weight residual 111.36 104.33 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" C ASP A 333 " ideal model delta sigma weight residual 111.54 120.21 -8.67 1.36e+00 5.41e-01 4.06e+01 ... (remaining 31049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 12904 15.23 - 30.47: 708 30.47 - 45.70: 134 45.70 - 60.94: 26 60.94 - 76.17: 14 Dihedral angle restraints: 13786 sinusoidal: 5729 harmonic: 8057 Sorted by residual: dihedral pdb=" CA SER B 209 " pdb=" C SER B 209 " pdb=" N PHE B 210 " pdb=" CA PHE B 210 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3201 0.114 - 0.228: 167 0.228 - 0.342: 9 0.342 - 0.456: 1 0.456 - 0.570: 1 Chirality restraints: 3379 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA TRP A 256 " pdb=" N TRP A 256 " pdb=" C TRP A 256 " pdb=" CB TRP A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP A1312 " pdb=" N TRP A1312 " pdb=" C TRP A1312 " pdb=" CB TRP A1312 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 3376 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1256 " -0.027 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A1256 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A1256 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A1256 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A1256 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1256 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A1256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1256 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 98 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C MET B 98 " 0.062 2.00e-02 2.50e+03 pdb=" O MET B 98 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 99 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1337 " -0.024 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A1337 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A1337 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A1337 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1337 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1337 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1337 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1337 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1337 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A1337 " 0.001 2.00e-02 2.50e+03 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 319 2.64 - 3.21: 19009 3.21 - 3.77: 34474 3.77 - 4.34: 48773 4.34 - 4.90: 79619 Nonbonded interactions: 182194 Sorted by model distance: nonbonded pdb=" O ASN E 458 " pdb=" ND2 ASN E 458 " model vdw 2.077 3.120 nonbonded pdb=" OE1 GLN A1188 " pdb=" OH TYR B 59 " model vdw 2.250 3.040 nonbonded pdb=" SG CYS A1126 " pdb=" N VAL A1172 " model vdw 2.252 3.480 nonbonded pdb=" OG1 THR A1101 " pdb=" O VAL A1172 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 221 " pdb=" OD1 ASP B 223 " model vdw 2.264 3.040 ... (remaining 182189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.850 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.009 0.088 22941 Z= 0.564 Angle : 1.053 13.026 31054 Z= 0.613 Chirality : 0.059 0.570 3379 Planarity : 0.007 0.075 3928 Dihedral : 10.427 76.174 8592 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.33 % Rotamer: Outliers : 0.58 % Allowed : 2.37 % Favored : 97.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.12), residues: 2713 helix: -3.92 (0.09), residues: 867 sheet: -2.30 (0.20), residues: 572 loop : -2.91 (0.14), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A1337 HIS 0.024 0.003 HIS A1307 PHE 0.044 0.004 PHE A1074 TYR 0.064 0.004 TYR A1256 ARG 0.012 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 681 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9022 (t) cc_final: 0.8751 (m) REVERT: A 104 SER cc_start: 0.8418 (t) cc_final: 0.7894 (m) REVERT: A 130 ASP cc_start: 0.7616 (t70) cc_final: 0.7391 (t70) REVERT: A 248 THR cc_start: 0.7331 (p) cc_final: 0.7125 (p) REVERT: A 354 MET cc_start: 0.3285 (mmm) cc_final: 0.2781 (mtm) REVERT: A 470 LEU cc_start: 0.8169 (tp) cc_final: 0.7938 (tt) REVERT: A 1186 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (mt) REVERT: A 1206 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7538 (pp) REVERT: A 1247 SER cc_start: 0.8246 (t) cc_final: 0.7839 (p) REVERT: B 72 TRP cc_start: 0.7251 (p-90) cc_final: 0.6976 (p-90) REVERT: B 290 THR cc_start: 0.7771 (m) cc_final: 0.7063 (m) REVERT: B 372 MET cc_start: 0.4304 (ttt) cc_final: 0.3989 (ttt) REVERT: C 28 LEU cc_start: 0.6073 (pt) cc_final: 0.5771 (mt) REVERT: C 70 HIS cc_start: 0.6092 (m-70) cc_final: 0.5851 (m170) REVERT: E 28 ASN cc_start: 0.5791 (t0) cc_final: 0.5531 (m-40) REVERT: E 320 PHE cc_start: 0.5321 (m-80) cc_final: 0.4977 (m-80) REVERT: F 29 PRO cc_start: 0.4086 (Cg_exo) cc_final: 0.3824 (Cg_endo) REVERT: F 58 VAL cc_start: 0.6516 (m) cc_final: 0.6264 (m) REVERT: F 541 LEU cc_start: 0.5710 (mt) cc_final: 0.5216 (pp) outliers start: 14 outliers final: 7 residues processed: 690 average time/residue: 0.4176 time to fit residues: 414.8630 Evaluate side-chains 369 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 360 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 252 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 679 HIS A 680 HIS A 866 HIS A 887 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 405 ASN B 416 ASN C 59 HIS E 162 ASN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS F 45 GLN F 162 ASN F 262 ASN F 289 HIS ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN F 461 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22941 Z= 0.227 Angle : 0.676 9.738 31054 Z= 0.356 Chirality : 0.044 0.175 3379 Planarity : 0.005 0.048 3928 Dihedral : 6.813 72.964 3143 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.58 % Allowed : 9.94 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.14), residues: 2713 helix: -1.95 (0.14), residues: 892 sheet: -1.73 (0.20), residues: 572 loop : -2.45 (0.15), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 35 HIS 0.014 0.001 HIS A1099 PHE 0.038 0.002 PHE E 384 TYR 0.028 0.002 TYR F 71 ARG 0.008 0.001 ARG A1248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 448 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8854 (t) cc_final: 0.8587 (m) REVERT: A 470 LEU cc_start: 0.8004 (tp) cc_final: 0.7614 (mp) REVERT: A 953 LEU cc_start: 0.7734 (tp) cc_final: 0.7065 (tt) REVERT: A 1206 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7480 (pp) REVERT: B 72 TRP cc_start: 0.7133 (p-90) cc_final: 0.6931 (p-90) REVERT: E 28 ASN cc_start: 0.5992 (t0) cc_final: 0.5423 (m-40) REVERT: E 122 MET cc_start: -0.0212 (tpp) cc_final: -0.1041 (tpt) REVERT: E 227 MET cc_start: 0.3796 (ppp) cc_final: 0.3333 (ttp) REVERT: E 343 TYR cc_start: 0.7401 (m-80) cc_final: 0.6677 (t80) REVERT: E 419 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5782 (mm-30) REVERT: F 93 MET cc_start: 0.7819 (mmt) cc_final: 0.7301 (mmt) REVERT: F 541 LEU cc_start: 0.6095 (mt) cc_final: 0.5492 (pp) outliers start: 62 outliers final: 26 residues processed: 492 average time/residue: 0.3703 time to fit residues: 275.0486 Evaluate side-chains 351 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 324 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 266 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS ** A1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 181 HIS B 199 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 22941 Z= 0.486 Angle : 0.807 14.757 31054 Z= 0.421 Chirality : 0.049 0.186 3379 Planarity : 0.006 0.070 3928 Dihedral : 6.940 72.493 3131 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.66 % Allowed : 12.98 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2713 helix: -1.02 (0.16), residues: 883 sheet: -1.80 (0.20), residues: 557 loop : -2.44 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1337 HIS 0.016 0.002 HIS A1099 PHE 0.029 0.003 PHE A1074 TYR 0.031 0.003 TYR E 346 ARG 0.009 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 355 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8163 (t80) cc_final: 0.7951 (t80) REVERT: A 80 SER cc_start: 0.9041 (t) cc_final: 0.8628 (m) REVERT: A 469 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8277 (mt) REVERT: A 470 LEU cc_start: 0.8266 (tp) cc_final: 0.7554 (mp) REVERT: A 685 HIS cc_start: 0.4942 (OUTLIER) cc_final: 0.4559 (m-70) REVERT: A 1058 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 1186 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 1206 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7623 (pp) REVERT: E 96 LEU cc_start: 0.4030 (OUTLIER) cc_final: 0.3775 (tp) REVERT: E 187 TRP cc_start: 0.4227 (t60) cc_final: 0.3648 (t60) REVERT: F 93 MET cc_start: 0.8186 (mmt) cc_final: 0.7534 (mmt) REVERT: F 308 LEU cc_start: 0.7341 (mt) cc_final: 0.7115 (tt) REVERT: F 382 MET cc_start: 0.8223 (mtp) cc_final: 0.8012 (mtp) REVERT: F 541 LEU cc_start: 0.6858 (mt) cc_final: 0.5859 (pp) outliers start: 88 outliers final: 53 residues processed: 426 average time/residue: 0.3552 time to fit residues: 232.7304 Evaluate side-chains 353 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 295 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 484 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS A1188 GLN B 69 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 325 GLN B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22941 Z= 0.219 Angle : 0.627 12.624 31054 Z= 0.327 Chirality : 0.043 0.165 3379 Planarity : 0.004 0.049 3928 Dihedral : 6.328 72.937 3129 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.08 % Allowed : 15.02 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), residues: 2713 helix: -0.45 (0.17), residues: 900 sheet: -1.85 (0.20), residues: 601 loop : -2.28 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 35 HIS 0.011 0.001 HIS C 114 PHE 0.031 0.002 PHE B 153 TYR 0.027 0.002 TYR E 450 ARG 0.006 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 352 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8923 (t) cc_final: 0.8627 (m) REVERT: A 469 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 470 LEU cc_start: 0.8070 (tp) cc_final: 0.7582 (mp) REVERT: A 584 MET cc_start: 0.5968 (mtt) cc_final: 0.5750 (mtt) REVERT: A 685 HIS cc_start: 0.4773 (OUTLIER) cc_final: 0.4455 (m-70) REVERT: A 990 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 1058 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 1206 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7445 (pp) REVERT: E 96 LEU cc_start: 0.3766 (OUTLIER) cc_final: 0.3515 (tp) REVERT: E 187 TRP cc_start: 0.4183 (t60) cc_final: 0.3820 (t60) REVERT: E 343 TYR cc_start: 0.7430 (m-80) cc_final: 0.6476 (m-80) REVERT: F 67 PHE cc_start: 0.5462 (m-80) cc_final: 0.5211 (m-80) REVERT: F 71 TYR cc_start: 0.4028 (t80) cc_final: 0.3692 (t80) REVERT: F 303 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7899 (mt0) REVERT: F 541 LEU cc_start: 0.6695 (mt) cc_final: 0.5945 (pp) outliers start: 74 outliers final: 40 residues processed: 410 average time/residue: 0.3277 time to fit residues: 212.4580 Evaluate side-chains 342 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 181 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22941 Z= 0.211 Angle : 0.610 11.160 31054 Z= 0.318 Chirality : 0.043 0.171 3379 Planarity : 0.004 0.047 3928 Dihedral : 6.140 73.026 3129 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.20 % Allowed : 15.68 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 2713 helix: -0.16 (0.17), residues: 899 sheet: -1.78 (0.20), residues: 602 loop : -2.14 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 35 HIS 0.013 0.001 HIS C 114 PHE 0.028 0.001 PHE A1074 TYR 0.036 0.002 TYR E 450 ARG 0.005 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 335 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8941 (t) cc_final: 0.8639 (m) REVERT: A 469 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 470 LEU cc_start: 0.8003 (tp) cc_final: 0.7509 (mp) REVERT: A 584 MET cc_start: 0.6104 (mtt) cc_final: 0.5832 (mtt) REVERT: A 685 HIS cc_start: 0.4585 (OUTLIER) cc_final: 0.4359 (m-70) REVERT: A 927 ARG cc_start: 0.4384 (mtp85) cc_final: 0.3952 (ttm170) REVERT: A 1058 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 1186 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 1206 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7567 (pp) REVERT: B 239 ILE cc_start: 0.7400 (mt) cc_final: 0.7194 (mt) REVERT: B 292 MET cc_start: 0.8063 (mmm) cc_final: 0.7593 (tpt) REVERT: E 96 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.3369 (tp) REVERT: E 138 MET cc_start: 0.4755 (mmm) cc_final: 0.4536 (mmt) REVERT: E 187 TRP cc_start: 0.4174 (t60) cc_final: 0.3822 (t60) REVERT: E 343 TYR cc_start: 0.7389 (m-80) cc_final: 0.7016 (m-80) REVERT: F 205 MET cc_start: 0.4951 (ttm) cc_final: 0.4636 (ttm) REVERT: F 244 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7377 (pm20) REVERT: F 303 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7910 (mt0) REVERT: F 327 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7784 (mt) REVERT: F 541 LEU cc_start: 0.6639 (mt) cc_final: 0.5967 (pp) outliers start: 77 outliers final: 44 residues processed: 391 average time/residue: 0.3200 time to fit residues: 198.2639 Evaluate side-chains 350 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 0.3980 chunk 235 optimal weight: 0.3980 chunk 51 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22941 Z= 0.235 Angle : 0.622 11.010 31054 Z= 0.322 Chirality : 0.043 0.171 3379 Planarity : 0.004 0.048 3928 Dihedral : 6.099 73.019 3129 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.08 % Allowed : 16.18 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2713 helix: 0.08 (0.17), residues: 901 sheet: -1.67 (0.20), residues: 595 loop : -2.12 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 143 HIS 0.013 0.001 HIS C 114 PHE 0.026 0.002 PHE A1074 TYR 0.037 0.002 TYR E 450 ARG 0.010 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 330 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8898 (t) cc_final: 0.8612 (m) REVERT: A 469 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 470 LEU cc_start: 0.8026 (tp) cc_final: 0.7488 (mp) REVERT: A 584 MET cc_start: 0.6227 (mtt) cc_final: 0.5896 (mtt) REVERT: A 679 HIS cc_start: 0.5834 (OUTLIER) cc_final: 0.5180 (m-70) REVERT: A 685 HIS cc_start: 0.4614 (OUTLIER) cc_final: 0.4396 (m-70) REVERT: A 927 ARG cc_start: 0.4338 (mtp85) cc_final: 0.4069 (ttm170) REVERT: A 1186 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8807 (mt) REVERT: A 1206 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7422 (pp) REVERT: B 229 TRP cc_start: 0.7374 (m100) cc_final: 0.7060 (m100) REVERT: B 292 MET cc_start: 0.8089 (mmm) cc_final: 0.7609 (tpt) REVERT: E 90 ARG cc_start: 0.6314 (mmm-85) cc_final: 0.5746 (tmt170) REVERT: E 138 MET cc_start: 0.4590 (mmm) cc_final: 0.2884 (mtt) REVERT: E 187 TRP cc_start: 0.4050 (t60) cc_final: 0.3773 (t60) REVERT: E 343 TYR cc_start: 0.7426 (m-80) cc_final: 0.7000 (m-80) REVERT: F 93 MET cc_start: 0.8222 (mmt) cc_final: 0.7862 (mmt) REVERT: F 244 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7241 (pm20) REVERT: F 303 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7967 (mt0) REVERT: F 541 LEU cc_start: 0.6636 (mt) cc_final: 0.5956 (pp) outliers start: 74 outliers final: 51 residues processed: 379 average time/residue: 0.3286 time to fit residues: 199.5950 Evaluate side-chains 353 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 297 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN F 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22941 Z= 0.336 Angle : 0.687 12.187 31054 Z= 0.356 Chirality : 0.046 0.263 3379 Planarity : 0.004 0.049 3928 Dihedral : 6.299 72.824 3129 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.29 % Allowed : 16.85 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2713 helix: 0.10 (0.17), residues: 890 sheet: -1.73 (0.20), residues: 597 loop : -2.10 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 143 HIS 0.019 0.001 HIS C 114 PHE 0.041 0.002 PHE B 153 TYR 0.046 0.002 TYR F 378 ARG 0.008 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 317 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9001 (t) cc_final: 0.8650 (m) REVERT: A 469 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8194 (mt) REVERT: A 470 LEU cc_start: 0.8009 (tp) cc_final: 0.7431 (mp) REVERT: A 584 MET cc_start: 0.6341 (mtt) cc_final: 0.5993 (mtt) REVERT: A 679 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5791 (m-70) REVERT: A 685 HIS cc_start: 0.4503 (OUTLIER) cc_final: 0.4265 (m-70) REVERT: A 927 ARG cc_start: 0.4583 (mtp85) cc_final: 0.4245 (ttm170) REVERT: A 1186 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8845 (mt) REVERT: A 1206 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7622 (pp) REVERT: B 130 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5020 (mt-10) REVERT: B 229 TRP cc_start: 0.7429 (m100) cc_final: 0.7179 (m100) REVERT: B 292 MET cc_start: 0.8178 (mmm) cc_final: 0.7750 (tpt) REVERT: C 70 HIS cc_start: 0.6198 (m170) cc_final: 0.5887 (m170) REVERT: E 90 ARG cc_start: 0.6073 (mmm-85) cc_final: 0.5621 (tmt170) REVERT: E 93 MET cc_start: 0.1912 (OUTLIER) cc_final: 0.1355 (mmm) REVERT: E 187 TRP cc_start: 0.4175 (t60) cc_final: 0.3842 (t60) REVERT: E 343 TYR cc_start: 0.7329 (m-80) cc_final: 0.7043 (m-80) REVERT: F 110 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6026 (mt-10) REVERT: F 303 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7989 (mt0) REVERT: F 327 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7719 (mt) outliers start: 79 outliers final: 56 residues processed: 376 average time/residue: 0.3220 time to fit residues: 192.3574 Evaluate side-chains 361 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 297 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 TYR Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 205 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22941 Z= 0.189 Angle : 0.626 12.367 31054 Z= 0.321 Chirality : 0.043 0.206 3379 Planarity : 0.004 0.049 3928 Dihedral : 5.996 73.320 3129 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.75 % Allowed : 17.97 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2713 helix: 0.25 (0.17), residues: 895 sheet: -1.63 (0.21), residues: 582 loop : -2.04 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 143 HIS 0.012 0.001 HIS C 114 PHE 0.028 0.001 PHE A1074 TYR 0.042 0.002 TYR F 378 ARG 0.006 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 337 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8877 (t) cc_final: 0.8648 (m) REVERT: A 470 LEU cc_start: 0.7835 (tp) cc_final: 0.7404 (mp) REVERT: A 584 MET cc_start: 0.6312 (mtt) cc_final: 0.5942 (mtt) REVERT: A 1186 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 1206 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7756 (pp) REVERT: B 130 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4863 (mt-10) REVERT: B 229 TRP cc_start: 0.7215 (m100) cc_final: 0.6993 (m100) REVERT: B 292 MET cc_start: 0.8115 (mmm) cc_final: 0.7596 (tpt) REVERT: C 70 HIS cc_start: 0.6049 (m170) cc_final: 0.5751 (m170) REVERT: E 93 MET cc_start: 0.1856 (OUTLIER) cc_final: 0.0892 (mmm) REVERT: E 122 MET cc_start: 0.0317 (tpp) cc_final: 0.0023 (tpp) REVERT: E 343 TYR cc_start: 0.7287 (m-80) cc_final: 0.6913 (m-80) REVERT: F 110 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6080 (mt-10) REVERT: F 244 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7069 (pm20) REVERT: F 303 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7833 (mt0) outliers start: 66 outliers final: 50 residues processed: 384 average time/residue: 0.3305 time to fit residues: 203.8335 Evaluate side-chains 353 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 299 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 68 TRP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 TYR Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 219 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 HIS ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN F 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 22941 Z= 0.562 Angle : 0.865 15.512 31054 Z= 0.444 Chirality : 0.051 0.254 3379 Planarity : 0.006 0.055 3928 Dihedral : 6.878 72.718 3129 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.04 % Allowed : 18.68 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2713 helix: -0.08 (0.17), residues: 886 sheet: -1.98 (0.20), residues: 600 loop : -2.19 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP E 187 HIS 0.020 0.002 HIS C 114 PHE 0.036 0.003 PHE A1074 TYR 0.044 0.003 TYR E 450 ARG 0.018 0.001 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 302 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9101 (t) cc_final: 0.8686 (m) REVERT: A 237 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 469 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 470 LEU cc_start: 0.8193 (tp) cc_final: 0.7469 (mp) REVERT: A 584 MET cc_start: 0.6610 (mtt) cc_final: 0.6218 (mtt) REVERT: A 1058 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 1186 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8877 (mt) REVERT: A 1206 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7713 (pp) REVERT: A 1383 MET cc_start: 0.7414 (mmm) cc_final: 0.7020 (mmm) REVERT: B 130 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5519 (mt-10) REVERT: B 292 MET cc_start: 0.8289 (mmm) cc_final: 0.7679 (tpt) REVERT: B 411 MET cc_start: 0.7429 (mtm) cc_final: 0.7204 (mtt) REVERT: C 70 HIS cc_start: 0.6651 (m170) cc_final: 0.6401 (m170) REVERT: C 85 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5142 (tp) REVERT: E 90 ARG cc_start: 0.6321 (mmm-85) cc_final: 0.5914 (tmt170) REVERT: E 505 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6691 (tt0) REVERT: F 110 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6500 (tt0) REVERT: F 303 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8177 (mt0) outliers start: 73 outliers final: 49 residues processed: 358 average time/residue: 0.3274 time to fit residues: 184.2732 Evaluate side-chains 334 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 248 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22941 Z= 0.225 Angle : 0.684 13.396 31054 Z= 0.351 Chirality : 0.045 0.185 3379 Planarity : 0.004 0.051 3928 Dihedral : 6.389 73.309 3129 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.33 % Allowed : 19.47 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2713 helix: 0.17 (0.17), residues: 891 sheet: -1.74 (0.21), residues: 572 loop : -2.06 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP E 143 HIS 0.012 0.001 HIS C 114 PHE 0.027 0.002 PHE F 530 TYR 0.040 0.002 TYR E 450 ARG 0.008 0.001 ARG E 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5426 Ramachandran restraints generated. 2713 Oldfield, 0 Emsley, 2713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 314 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.8960 (t) cc_final: 0.8655 (m) REVERT: A 237 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8096 (p) REVERT: A 469 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 470 LEU cc_start: 0.7885 (tp) cc_final: 0.7458 (mp) REVERT: A 584 MET cc_start: 0.6423 (mtt) cc_final: 0.6030 (mtt) REVERT: A 811 PHE cc_start: 0.7211 (t80) cc_final: 0.6907 (t80) REVERT: A 1206 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7600 (pp) REVERT: A 1383 MET cc_start: 0.7171 (mmm) cc_final: 0.6762 (mmm) REVERT: B 130 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.5090 (mt-10) REVERT: B 229 TRP cc_start: 0.7406 (m100) cc_final: 0.7194 (m100) REVERT: B 292 MET cc_start: 0.8103 (mmm) cc_final: 0.7604 (tpt) REVERT: B 411 MET cc_start: 0.7120 (mtm) cc_final: 0.6862 (mtt) REVERT: C 17 ILE cc_start: 0.7651 (mt) cc_final: 0.7439 (mt) REVERT: C 70 HIS cc_start: 0.6120 (m170) cc_final: 0.5851 (m170) REVERT: C 85 LEU cc_start: 0.5516 (mm) cc_final: 0.5160 (tp) REVERT: E 239 PRO cc_start: 0.5896 (Cg_exo) cc_final: 0.5593 (Cg_endo) REVERT: E 505 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6492 (tt0) REVERT: F 110 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6272 (tt0) REVERT: F 303 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7897 (mt0) REVERT: F 476 LEU cc_start: 0.7899 (tt) cc_final: 0.7676 (tt) REVERT: F 487 ARG cc_start: 0.6958 (mmp80) cc_final: 0.6737 (mmp80) outliers start: 56 outliers final: 41 residues processed: 356 average time/residue: 0.3185 time to fit residues: 181.6859 Evaluate side-chains 338 residues out of total 2404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 403 GLU Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 531 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 221 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 GLN ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.157220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126651 restraints weight = 39102.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125931 restraints weight = 35785.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127410 restraints weight = 27556.669| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22941 Z= 0.297 Angle : 0.716 13.819 31054 Z= 0.367 Chirality : 0.045 0.194 3379 Planarity : 0.005 0.055 3928 Dihedral : 6.390 73.167 3129 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.29 % Allowed : 19.93 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2713 helix: 0.16 (0.17), residues: 908 sheet: -1.75 (0.21), residues: 581 loop : -2.12 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP F 187 HIS 0.017 0.001 HIS B 310 PHE 0.032 0.002 PHE F 67 TYR 0.041 0.002 TYR E 450 ARG 0.007 0.001 ARG A1049 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4900.36 seconds wall clock time: 88 minutes 18.52 seconds (5298.52 seconds total)