Starting phenix.real_space_refine on Sun Sep 13 09:50:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2026/6uro_20861.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: 4.54, per 1000 atoms: 0.20 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: 1.36 Conformation dependent library (CDL) restraints added in 1.0 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: 0.70 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: 5.25 Time building geometry restraints manager: 1.85 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: 30031 2.61 - 5.21: 897 5.21 - 7.82: 103 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: 12866 15.23 - 30.47: 721 30.47 - 45.70: 133 45.70 - 60.94: 38 60.94 - 76.17: 20 Dihedral angle restraints: 13778 sinusoidal: 5721 harmonic: 8057 Sorted by residual: dihedral pdb=" C4' A D 2 " pdb=" C3' A D 2 " pdb=" C2' A D 2 " pdb=" C1' A D 2 " ideal model delta sinusoidal sigma weight residual 36.35 -37.68 74.03 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' A D 4 " pdb=" C3' A D 4 " pdb=" C2' A D 4 " pdb=" C1' A D 4 " ideal model delta sinusoidal sigma weight residual 36.34 -37.18 73.53 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' A D 6 " pdb=" C3' A D 6 " pdb=" C2' A D 6 " pdb=" C1' A D 6 " ideal model delta sinusoidal sigma weight residual 36.35 -37.16 73.50 1 3.10e+00 1.04e-01 7.15e+02 ... (remaining 13775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3181 0.114 - 0.228: 170 0.228 - 0.342: 26 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.790 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 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 : 0.010 0.694 22950 Z= 0.413 Angle : 1.063 13.026 31054 Z= 0.616 Chirality : 0.062 0.570 3379 Planarity : 0.007 0.075 3928 Dihedral : 10.845 76.174 8584 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.81 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG B 404 TYR 0.064 0.004 TYR A1256 PHE 0.044 0.004 PHE A1074 TRP 0.059 0.004 TRP A1337 HIS 0.024 0.003 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.37 (22941) covalent geometry : angle 1.06291 / 0.62 (31054) hydrogen bonds : bond 0.29285 / 19.51 ( 829) hydrogen bonds : angle 10.23187 / 7.05 ( 2376) metal coordination : bond 0.27473 / 17.50 ( 9) *********************** 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 to be fit. rotamer outliers: 14 poor density : 681 time to evaluate : 0.757 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: A 80 SER cc_start: 0.9022 (t) cc_final: 0.8751 (m) REVERT: A 104 SER cc_start: 0.8417 (t) cc_final: 0.7893 (m) REVERT: A 130 ASP cc_start: 0.7617 (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: 0.2782 (mtm) REVERT: A 470 LEU cc_start: 0.8169 (tp) cc_final: 0.7937 (tt) REVERT: A 1186 ILE cc_start: 0.9181 (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: 0.7840 (p) REVERT: B 72 TRP cc_start: 0.7251 (p-90) cc_final: 0.6975 (p-90) REVERT: B 290 THR cc_start: 0.7771 (m) cc_final: 0.7060 (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: 0.5770 (mt) REVERT: C 70 HIS cc_start: 0.6092 (m-70) cc_final: 0.5852 (m170) REVERT: E 28 ASN cc_start: 0.5791 (t0) cc_final: 0.5533 (m-40) REVERT: E 320 PHE cc_start: 0.5321 (m-80) cc_final: 0.4978 (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: 0.1894 time to fit residues: 190.8177 Evaluate side-chains 369 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 360 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.169185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136831 restraints weight = 38386.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135189 restraints weight = 31160.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136795 restraints weight = 25885.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136924 restraints weight = 20674.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137118 restraints weight = 17393.346| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 22950 Z= 0.165 Angle : 0.721 10.930 31054 Z= 0.372 Chirality : 0.051 0.597 3379 Planarity : 0.005 0.049 3928 Dihedral : 6.950 62.441 3135 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.70 % Allowed : 9.98 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.14), residues: 2713 helix: -1.96 (0.14), residues: 892 sheet: -1.76 (0.20), residues: 575 loop : -2.44 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1248 TYR 0.029 0.002 TYR F 71 PHE 0.038 0.002 PHE E 384 TRP 0.033 0.002 TRP E 35 HIS 0.020 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22941) covalent geometry : angle 0.72138 / 0.37 (31054) hydrogen bonds : bond 0.04916 / 3.27 ( 829) hydrogen bonds : angle 5.93655 / 4.14 ( 2376) metal coordination : bond 0.04867 / 2.72 ( 9) *********************** 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 512 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 447 time to evaluate : 0.864 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 24 ASN cc_start: 0.8390 (p0) cc_final: 0.8135 (p0) REVERT: A 80 SER cc_start: 0.8991 (t) cc_final: 0.8646 (m) REVERT: A 248 THR cc_start: 0.8129 (p) cc_final: 0.7792 (p) REVERT: A 470 LEU cc_start: 0.8140 (tp) cc_final: 0.7625 (mp) REVERT: A 953 LEU cc_start: 0.7775 (tp) cc_final: 0.7054 (tt) REVERT: A 998 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 1206 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 126 ARG cc_start: 0.7327 (mmp80) cc_final: 0.7031 (mmp80) REVERT: B 273 TRP cc_start: 0.6635 (m100) cc_final: 0.6380 (m100) REVERT: E 28 ASN cc_start: 0.6258 (t0) cc_final: 0.5676 (m-40) REVERT: E 35 TRP cc_start: 0.3475 (m100) cc_final: 0.3064 (m100) REVERT: E 52 LYS cc_start: 0.7236 (pttp) cc_final: 0.6658 (mmtt) REVERT: E 122 MET cc_start: -0.0916 (tpp) cc_final: -0.1310 (tpp) REVERT: E 214 MET cc_start: 0.0575 (tpt) cc_final: 0.0167 (tpt) REVERT: E 227 MET cc_start: 0.4965 (ppp) cc_final: 0.4161 (ttp) REVERT: E 343 TYR cc_start: 0.7954 (m-80) cc_final: 0.6846 (t80) REVERT: E 346 TYR cc_start: 0.7155 (t80) cc_final: 0.6574 (t80) REVERT: E 419 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5891 (mm-30) REVERT: F 86 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8598 (mtmt) REVERT: F 93 MET cc_start: 0.7789 (mmt) cc_final: 0.7099 (mmt) REVERT: F 218 ARG cc_start: 0.5428 (tmm-80) cc_final: 0.4675 (mtm-85) REVERT: F 533 LEU cc_start: 0.7459 (mt) cc_final: 0.7168 (mp) REVERT: F 541 LEU cc_start: 0.6987 (mt) cc_final: 0.5822 (pp) outliers start: 65 outliers final: 27 residues processed: 495 average time/residue: 0.1589 time to fit residues: 120.8869 Evaluate side-chains 355 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 326 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 928 VAL Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 998 ILE 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 352 SER 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 119 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 115 optimal weight: 0.0670 chunk 134 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 HIS A 679 HIS A 858 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS A1177 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 171 HIS B 181 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN 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 E 461 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133956 restraints weight = 38823.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133051 restraints weight = 39312.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134488 restraints weight = 33821.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134633 restraints weight = 24001.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134907 restraints weight = 21880.654| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22950 Z= 0.180 Angle : 0.670 10.556 31054 Z= 0.346 Chirality : 0.047 0.471 3379 Planarity : 0.005 0.093 3928 Dihedral : 6.849 112.284 3123 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.91 % Allowed : 13.06 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.15), residues: 2713 helix: -0.97 (0.16), residues: 903 sheet: -1.69 (0.20), residues: 569 loop : -2.34 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 112 TYR 0.027 0.002 TYR F 172 PHE 0.022 0.002 PHE F 88 TRP 0.020 0.002 TRP E 258 HIS 0.012 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (22941) covalent geometry : angle 0.67031 / 0.35 (31054) hydrogen bonds : bond 0.04121 / 2.69 ( 829) hydrogen bonds : angle 5.46000 / 3.79 ( 2376) metal coordination : bond 0.01894 / 1.39 ( 9) *********************** 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 430 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 0.873 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 24 ASN cc_start: 0.8362 (p0) cc_final: 0.8026 (p0) REVERT: A 80 SER cc_start: 0.9089 (t) cc_final: 0.8630 (m) REVERT: A 144 ASP cc_start: 0.5871 (t0) cc_final: 0.5061 (t0) REVERT: A 148 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7141 (mtm-85) REVERT: A 469 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 470 LEU cc_start: 0.8127 (tp) cc_final: 0.7581 (mp) REVERT: A 872 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7198 (pp) REVERT: A 1058 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 1206 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 1215 MET cc_start: 0.6333 (mtm) cc_final: 0.6012 (mtp) REVERT: A 1294 MET cc_start: 0.6421 (mmm) cc_final: 0.6176 (mmm) REVERT: B 99 LEU cc_start: 0.8028 (mt) cc_final: 0.7697 (mt) REVERT: B 104 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (t0) REVERT: B 126 ARG cc_start: 0.7045 (mmp80) cc_final: 0.6784 (mmp80) REVERT: B 411 MET cc_start: 0.7759 (mtm) cc_final: 0.7523 (mtm) REVERT: C 28 LEU cc_start: 0.6467 (pp) cc_final: 0.5722 (mt) REVERT: C 69 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6395 (ttpt) REVERT: C 115 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.5922 (tt) REVERT: E 28 ASN cc_start: 0.6525 (t0) cc_final: 0.5847 (m-40) REVERT: E 35 TRP cc_start: 0.3680 (m100) cc_final: 0.3339 (m100) REVERT: E 52 LYS cc_start: 0.6811 (pttp) cc_final: 0.6408 (mmtt) REVERT: E 68 TRP cc_start: 0.6944 (m100) cc_final: 0.6626 (t60) REVERT: E 122 MET cc_start: -0.0240 (tpp) cc_final: -0.0634 (tpp) REVERT: E 187 TRP cc_start: 0.4848 (t60) cc_final: 0.4090 (t60) REVERT: E 227 MET cc_start: 0.4701 (ppp) cc_final: 0.3699 (ttm) REVERT: F 54 TYR cc_start: 0.4924 (m-80) cc_final: 0.4508 (m-80) REVERT: F 71 TYR cc_start: 0.3753 (t80) cc_final: 0.3228 (t80) REVERT: F 205 MET cc_start: 0.5754 (ttm) cc_final: 0.5284 (ttm) REVERT: F 303 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7701 (mt0) REVERT: F 541 LEU cc_start: 0.7019 (mt) cc_final: 0.5989 (pp) outliers start: 70 outliers final: 39 residues processed: 413 average time/residue: 0.1559 time to fit residues: 100.0918 Evaluate side-chains 350 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR 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 480 VAL 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 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 943 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 1063 ASP 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 1245 LEU 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 151 PHE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 177 LEU 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 389 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 39 ILE 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 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 69 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1188 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN E 461 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.159305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.127980 restraints weight = 38987.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125482 restraints weight = 34427.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127064 restraints weight = 31075.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127484 restraints weight = 21475.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127684 restraints weight = 19795.863| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22950 Z= 0.248 Angle : 0.722 13.438 31054 Z= 0.372 Chirality : 0.049 0.441 3379 Planarity : 0.005 0.056 3928 Dihedral : 6.954 133.721 3121 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.45 % Allowed : 14.06 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.15), residues: 2713 helix: -0.37 (0.17), residues: 880 sheet: -1.72 (0.20), residues: 574 loop : -2.27 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 387 TYR 0.031 0.002 TYR F 343 PHE 0.034 0.002 PHE E 384 TRP 0.025 0.002 TRP E 258 HIS 0.012 0.002 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (22941) covalent geometry : angle 0.72232 / 0.37 (31054) hydrogen bonds : bond 0.04080 / 2.66 ( 829) hydrogen bonds : angle 5.46044 / 3.77 ( 2376) metal coordination : bond 0.01787 / 1.36 ( 9) *********************** 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 428 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9117 (t) cc_final: 0.8675 (m) REVERT: A 469 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 470 LEU cc_start: 0.8299 (tp) cc_final: 0.7616 (mp) REVERT: A 584 MET cc_start: 0.5905 (mtt) cc_final: 0.5602 (mtt) REVERT: A 679 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4811 (m-70) REVERT: A 685 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5736 (m-70) REVERT: A 694 LYS cc_start: 0.7558 (mttt) cc_final: 0.7222 (mmtt) REVERT: A 872 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7536 (pp) REVERT: A 885 GLN cc_start: 0.7270 (mm110) cc_final: 0.7023 (pt0) REVERT: A 990 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 1058 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 1186 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 1206 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7552 (pp) REVERT: A 1217 SER cc_start: 0.5439 (m) cc_final: 0.5159 (t) REVERT: B 103 MET cc_start: 0.7862 (mmt) cc_final: 0.7540 (mmt) REVERT: B 411 MET cc_start: 0.7778 (mtm) cc_final: 0.7474 (mtm) REVERT: C 115 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.5958 (tt) REVERT: E 187 TRP cc_start: 0.5312 (t60) cc_final: 0.4413 (t60) REVERT: E 214 MET cc_start: 0.0672 (tpt) cc_final: 0.0280 (tpt) REVERT: E 274 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7509 (mmtt) REVERT: E 542 LYS cc_start: 0.6938 (tttt) cc_final: 0.6534 (tptt) REVERT: F 93 MET cc_start: 0.8083 (mmt) cc_final: 0.7555 (mmt) REVERT: F 205 MET cc_start: 0.5427 (ttm) cc_final: 0.5086 (ttm) REVERT: F 303 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7819 (mt0) REVERT: F 314 MET cc_start: 0.6437 (tpp) cc_final: 0.6158 (ttt) REVERT: F 396 MET cc_start: 0.7523 (mmt) cc_final: 0.7238 (mmt) REVERT: F 541 LEU cc_start: 0.7379 (mt) cc_final: 0.6170 (pp) outliers start: 83 outliers final: 49 residues processed: 411 average time/residue: 0.1532 time to fit residues: 98.2316 Evaluate side-chains 345 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 657 VAL 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 709 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1275 ASP 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 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 142 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 213 THR 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 352 SER Chi-restraints excluded: chain B residue 386 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 326 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 451 ILE 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 484 ILE Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 236 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 310 HIS 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130723 restraints weight = 38600.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128776 restraints weight = 33085.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130180 restraints weight = 24943.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130799 restraints weight = 18905.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130855 restraints weight = 17804.013| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22950 Z= 0.134 Angle : 0.615 11.775 31054 Z= 0.317 Chirality : 0.045 0.318 3379 Planarity : 0.004 0.046 3928 Dihedral : 6.648 135.395 3121 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.75 % Allowed : 15.81 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.16), residues: 2713 helix: -0.01 (0.17), residues: 879 sheet: -1.71 (0.20), residues: 597 loop : -2.09 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 56 TYR 0.031 0.002 TYR F 140 PHE 0.031 0.001 PHE B 153 TRP 0.052 0.002 TRP E 35 HIS 0.015 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (22941) covalent geometry : angle 0.61522 / 0.32 (31054) hydrogen bonds : bond 0.03569 / 2.32 ( 829) hydrogen bonds : angle 5.11936 / 3.54 ( 2376) metal coordination : bond 0.01069 / 0.77 ( 9) *********************** 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 405 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 339 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8433 (p0) cc_final: 0.8020 (p0) REVERT: A 80 SER cc_start: 0.9084 (t) cc_final: 0.8691 (m) REVERT: A 469 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8051 (mt) REVERT: A 470 LEU cc_start: 0.8102 (tp) cc_final: 0.7548 (mp) REVERT: A 584 MET cc_start: 0.5968 (mtt) cc_final: 0.5523 (mtt) REVERT: A 679 HIS cc_start: 0.5467 (OUTLIER) cc_final: 0.4956 (m-70) REVERT: A 685 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5681 (m-70) REVERT: A 872 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7152 (pp) REVERT: A 990 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 1058 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 1186 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8739 (mt) REVERT: A 1206 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7593 (pp) REVERT: A 1342 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: B 103 MET cc_start: 0.7689 (mmt) cc_final: 0.7300 (mmt) REVERT: B 292 MET cc_start: 0.8213 (mmm) cc_final: 0.7494 (tpt) REVERT: C 115 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6322 (tt) REVERT: E 28 ASN cc_start: 0.5889 (t0) cc_final: 0.5630 (p0) REVERT: E 52 LYS cc_start: 0.7216 (pttt) cc_final: 0.6633 (mmtt) REVERT: E 68 TRP cc_start: 0.7252 (m100) cc_final: 0.6671 (t60) REVERT: E 122 MET cc_start: -0.0445 (tpp) cc_final: -0.0846 (tpp) REVERT: E 187 TRP cc_start: 0.5444 (t60) cc_final: 0.4597 (t60) REVERT: E 419 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6217 (mm-30) REVERT: F 54 TYR cc_start: 0.6190 (m-80) cc_final: 0.5652 (t80) REVERT: F 71 TYR cc_start: 0.4358 (t80) cc_final: 0.3080 (t80) REVERT: F 93 MET cc_start: 0.8081 (mmt) cc_final: 0.7612 (mmt) REVERT: F 205 MET cc_start: 0.5597 (ttm) cc_final: 0.5180 (ttm) REVERT: F 303 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7813 (mt0) REVERT: F 314 MET cc_start: 0.6456 (tpp) cc_final: 0.6025 (ttm) REVERT: F 541 LEU cc_start: 0.7500 (mt) cc_final: 0.6306 (pp) outliers start: 66 outliers final: 40 residues processed: 390 average time/residue: 0.1366 time to fit residues: 86.3894 Evaluate side-chains 344 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 241 VAL 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 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 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 794 MET Chi-restraints excluded: chain A residue 872 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 1085 GLU 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 1310 THR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 44 ASP 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 142 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 342 VAL 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 326 ASN Chi-restraints excluded: chain F residue 57 LEU 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 457 LEU Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 18 optimal weight: 0.0370 chunk 261 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.161179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129856 restraints weight = 39057.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128299 restraints weight = 33940.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129980 restraints weight = 28712.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130089 restraints weight = 21358.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130467 restraints weight = 18252.372| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22950 Z= 0.169 Angle : 0.640 11.444 31054 Z= 0.328 Chirality : 0.046 0.323 3379 Planarity : 0.004 0.048 3928 Dihedral : 6.598 134.619 3121 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.33 % Allowed : 16.01 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2713 helix: 0.15 (0.17), residues: 876 sheet: -1.63 (0.20), residues: 594 loop : -2.00 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 386 TYR 0.039 0.002 TYR E 450 PHE 0.029 0.002 PHE A1074 TRP 0.038 0.002 TRP E 143 HIS 0.007 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22941) covalent geometry : angle 0.64038 / 0.33 (31054) hydrogen bonds : bond 0.03572 / 2.34 ( 829) hydrogen bonds : angle 5.07402 / 3.50 ( 2376) metal coordination : bond 0.01246 / 0.93 ( 9) *********************** 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 387 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 307 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8474 (p0) cc_final: 0.8068 (p0) REVERT: A 80 SER cc_start: 0.9129 (t) cc_final: 0.8718 (m) REVERT: A 469 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8075 (mt) REVERT: A 470 LEU cc_start: 0.8131 (tp) cc_final: 0.7536 (mp) REVERT: A 584 MET cc_start: 0.6103 (mtt) cc_final: 0.5623 (mtt) REVERT: A 679 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.5025 (m-70) REVERT: A 685 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.5682 (m-70) REVERT: A 694 LYS cc_start: 0.7511 (mttt) cc_final: 0.7183 (mmtt) REVERT: A 990 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 1186 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8744 (mt) REVERT: A 1206 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7509 (pp) REVERT: A 1342 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: B 292 MET cc_start: 0.8212 (mmm) cc_final: 0.7503 (tpt) REVERT: C 115 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6156 (tt) REVERT: E 28 ASN cc_start: 0.5817 (t0) cc_final: 0.4922 (m-40) REVERT: E 52 LYS cc_start: 0.7112 (pttt) cc_final: 0.6737 (mmtt) REVERT: E 68 TRP cc_start: 0.7128 (m100) cc_final: 0.6719 (t60) REVERT: E 122 MET cc_start: -0.0347 (tpp) cc_final: -0.0746 (tpp) REVERT: E 138 MET cc_start: 0.5907 (mmm) cc_final: 0.3705 (mtt) REVERT: E 187 TRP cc_start: 0.5195 (t60) cc_final: 0.4436 (t60) REVERT: E 214 MET cc_start: 0.0790 (tpt) cc_final: 0.0354 (tpt) REVERT: F 93 MET cc_start: 0.8132 (mmt) cc_final: 0.7690 (mmt) REVERT: F 205 MET cc_start: 0.5824 (ttm) cc_final: 0.5357 (ttm) REVERT: F 303 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7816 (mt0) REVERT: F 314 MET cc_start: 0.6526 (tpp) cc_final: 0.6226 (ttm) REVERT: F 541 LEU cc_start: 0.7372 (mt) cc_final: 0.6276 (pp) outliers start: 80 outliers final: 51 residues processed: 370 average time/residue: 0.1355 time to fit residues: 81.1807 Evaluate side-chains 349 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 794 MET Chi-restraints excluded: chain A residue 943 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 44 ASP 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 142 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 172 ASN 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 C residue 114 HIS Chi-restraints excluded: chain C residue 115 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 405 THR 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 57 LEU 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 171 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 858 GLN ** 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 310 HIS B 416 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130157 restraints weight = 38938.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129020 restraints weight = 36731.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130327 restraints weight = 30761.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130911 restraints weight = 21713.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130990 restraints weight = 21023.224| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22950 Z= 0.165 Angle : 0.636 11.069 31054 Z= 0.328 Chirality : 0.046 0.308 3379 Planarity : 0.004 0.048 3928 Dihedral : 6.528 134.118 3121 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.20 % Allowed : 16.56 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2713 helix: 0.26 (0.17), residues: 880 sheet: -1.60 (0.20), residues: 596 loop : -1.95 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 40 TYR 0.038 0.002 TYR E 450 PHE 0.022 0.002 PHE A1074 TRP 0.052 0.002 TRP E 143 HIS 0.007 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (22941) covalent geometry : angle 0.63627 / 0.33 (31054) hydrogen bonds : bond 0.03508 / 2.30 ( 829) hydrogen bonds : angle 5.03123 / 3.48 ( 2376) metal coordination : bond 0.00912 / 0.65 ( 9) *********************** 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 399 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 322 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8469 (p0) cc_final: 0.8061 (p0) REVERT: A 80 SER cc_start: 0.9153 (t) cc_final: 0.8728 (m) REVERT: A 469 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8011 (mt) REVERT: A 470 LEU cc_start: 0.8097 (tp) cc_final: 0.7545 (mp) REVERT: A 584 MET cc_start: 0.6297 (mtt) cc_final: 0.5805 (mtt) REVERT: A 679 HIS cc_start: 0.5530 (OUTLIER) cc_final: 0.5078 (m-70) REVERT: A 685 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.5470 (m-70) REVERT: A 694 LYS cc_start: 0.7551 (mttt) cc_final: 0.7205 (mmtt) REVERT: A 990 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8039 (t80) REVERT: A 1186 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8753 (mt) REVERT: A 1206 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7530 (pp) REVERT: B 103 MET cc_start: 0.7915 (mmt) cc_final: 0.7660 (mmt) REVERT: B 292 MET cc_start: 0.8240 (mmm) cc_final: 0.7467 (tpt) REVERT: C 115 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6065 (tt) REVERT: E 28 ASN cc_start: 0.6106 (t0) cc_final: 0.5161 (m-40) REVERT: E 52 LYS cc_start: 0.7001 (pttt) cc_final: 0.6692 (mmtt) REVERT: E 68 TRP cc_start: 0.7077 (m100) cc_final: 0.6768 (t60) REVERT: E 122 MET cc_start: 0.0046 (tpp) cc_final: -0.0375 (tpp) REVERT: E 138 MET cc_start: 0.6111 (mmm) cc_final: 0.5795 (mmt) REVERT: E 187 TRP cc_start: 0.5012 (t60) cc_final: 0.4342 (t60) REVERT: E 214 MET cc_start: 0.0778 (tpt) cc_final: 0.0496 (tpt) REVERT: E 330 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7648 (ttp-170) REVERT: E 542 LYS cc_start: 0.7239 (tttt) cc_final: 0.6854 (tptt) REVERT: F 71 TYR cc_start: 0.4152 (t80) cc_final: 0.3464 (t80) REVERT: F 303 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7858 (mt0) REVERT: F 314 MET cc_start: 0.6535 (tpp) cc_final: 0.6215 (ttm) REVERT: F 541 LEU cc_start: 0.7422 (mt) cc_final: 0.6309 (pp) outliers start: 77 outliers final: 53 residues processed: 381 average time/residue: 0.1449 time to fit residues: 88.5357 Evaluate side-chains 346 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 286 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 LEU 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 320 ILE 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 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 612 ILE 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 794 MET Chi-restraints excluded: chain A residue 943 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 44 ASP 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 156 ILE 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 C residue 114 HIS Chi-restraints excluded: chain C residue 115 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 405 THR 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 54 TYR 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 Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 181 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS C 26 GLN ** E 45 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.159498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.128393 restraints weight = 38747.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127018 restraints weight = 31906.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128302 restraints weight = 26251.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129656 restraints weight = 20246.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129678 restraints weight = 18535.011| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22950 Z= 0.177 Angle : 0.668 14.238 31054 Z= 0.339 Chirality : 0.046 0.322 3379 Planarity : 0.004 0.052 3928 Dihedral : 6.532 133.593 3121 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.37 % Allowed : 16.47 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.16), residues: 2713 helix: 0.33 (0.18), residues: 879 sheet: -1.67 (0.20), residues: 599 loop : -1.94 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 40 TYR 0.035 0.002 TYR E 450 PHE 0.034 0.002 PHE E 384 TRP 0.046 0.002 TRP E 143 HIS 0.007 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (22941) covalent geometry : angle 0.66755 / 0.34 (31054) hydrogen bonds : bond 0.03533 / 2.33 ( 829) hydrogen bonds : angle 5.03938 / 3.49 ( 2376) metal coordination : bond 0.00891 / 0.64 ( 9) *********************** 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 387 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9132 (t) cc_final: 0.8724 (m) REVERT: A 469 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 470 LEU cc_start: 0.8058 (tp) cc_final: 0.7475 (mp) REVERT: A 584 MET cc_start: 0.6302 (mtt) cc_final: 0.5810 (mtt) REVERT: A 679 HIS cc_start: 0.5520 (OUTLIER) cc_final: 0.5213 (m-70) REVERT: A 685 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5457 (m-70) REVERT: A 694 LYS cc_start: 0.7572 (mttt) cc_final: 0.7147 (mmtt) REVERT: A 990 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8076 (t80) REVERT: A 1186 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8727 (mt) REVERT: A 1206 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7555 (pp) REVERT: B 130 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5560 (mt-10) REVERT: B 292 MET cc_start: 0.8255 (mmm) cc_final: 0.7479 (tpt) REVERT: C 99 TYR cc_start: 0.8227 (t80) cc_final: 0.7961 (t80) REVERT: C 115 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6108 (tt) REVERT: E 52 LYS cc_start: 0.7017 (pttt) cc_final: 0.6644 (mmtt) REVERT: E 90 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.6443 (ptm160) REVERT: E 122 MET cc_start: -0.0350 (tpp) cc_final: -0.0647 (tpp) REVERT: E 138 MET cc_start: 0.6373 (mmm) cc_final: 0.5831 (mmt) REVERT: E 187 TRP cc_start: 0.5117 (t60) cc_final: 0.4398 (t60) REVERT: E 330 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7697 (ttp-170) REVERT: E 542 LYS cc_start: 0.7325 (tttt) cc_final: 0.6923 (tptt) REVERT: F 303 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7960 (mt0) REVERT: F 314 MET cc_start: 0.6463 (tpp) cc_final: 0.6196 (ttm) outliers start: 81 outliers final: 57 residues processed: 367 average time/residue: 0.1435 time to fit residues: 85.2469 Evaluate side-chains 344 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 279 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 320 ILE 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 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 657 VAL 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 794 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 953 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 1261 MET Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1275 ASP 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 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 156 ILE 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 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 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 405 THR 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 95 VAL Chi-restraints excluded: chain F residue 98 ILE 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 Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 184 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 chunk 157 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 30.0000 chunk 233 optimal weight: 30.0000 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.160299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130274 restraints weight = 38828.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128807 restraints weight = 36811.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130368 restraints weight = 33666.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130634 restraints weight = 21975.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130857 restraints weight = 20352.153| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22950 Z= 0.166 Angle : 0.660 13.046 31054 Z= 0.337 Chirality : 0.046 0.306 3379 Planarity : 0.004 0.052 3928 Dihedral : 6.493 133.696 3121 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.08 % Allowed : 17.43 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2713 helix: 0.36 (0.18), residues: 875 sheet: -1.66 (0.20), residues: 595 loop : -1.87 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 386 TYR 0.037 0.002 TYR F 343 PHE 0.032 0.002 PHE E 384 TRP 0.082 0.002 TRP F 187 HIS 0.007 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22941) covalent geometry : angle 0.66037 / 0.34 (31054) hydrogen bonds : bond 0.03513 / 2.31 ( 829) hydrogen bonds : angle 5.00070 / 3.46 ( 2376) metal coordination : bond 0.00794 / 0.57 ( 9) *********************** 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 368 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9073 (t) cc_final: 0.8722 (m) REVERT: A 469 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 470 LEU cc_start: 0.7982 (tp) cc_final: 0.7458 (mp) REVERT: A 584 MET cc_start: 0.6469 (mtt) cc_final: 0.5965 (mtt) REVERT: A 685 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5224 (m-70) REVERT: A 694 LYS cc_start: 0.7551 (mttt) cc_final: 0.7212 (mmtt) REVERT: A 811 PHE cc_start: 0.7473 (t80) cc_final: 0.7027 (t80) REVERT: A 990 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8023 (t80) REVERT: A 1186 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8727 (mt) REVERT: A 1206 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7565 (pp) REVERT: A 1294 MET cc_start: 0.6480 (mmm) cc_final: 0.6270 (mmm) REVERT: B 130 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5391 (mt-10) REVERT: B 292 MET cc_start: 0.8274 (mmm) cc_final: 0.7508 (tpt) REVERT: C 99 TYR cc_start: 0.8100 (t80) cc_final: 0.7898 (t80) REVERT: C 115 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6209 (tt) REVERT: E 52 LYS cc_start: 0.6850 (pttt) cc_final: 0.6565 (mmtt) REVERT: E 68 TRP cc_start: 0.7043 (m100) cc_final: 0.6650 (t60) REVERT: E 122 MET cc_start: -0.0180 (tpp) cc_final: -0.0469 (tpp) REVERT: E 138 MET cc_start: 0.6317 (mmm) cc_final: 0.5868 (mmt) REVERT: E 319 LEU cc_start: 0.7854 (tt) cc_final: 0.7505 (tp) REVERT: E 405 THR cc_start: 0.5976 (OUTLIER) cc_final: 0.5541 (m) REVERT: E 528 TYR cc_start: 0.7879 (m-10) cc_final: 0.7592 (m-80) REVERT: E 542 LYS cc_start: 0.7288 (tttt) cc_final: 0.6873 (tptt) REVERT: F 187 TRP cc_start: 0.3905 (t60) cc_final: 0.3663 (t60) REVERT: F 303 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7804 (mt0) REVERT: F 314 MET cc_start: 0.6427 (tpp) cc_final: 0.6213 (ttm) outliers start: 74 outliers final: 55 residues processed: 351 average time/residue: 0.1463 time to fit residues: 82.8150 Evaluate side-chains 341 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 320 ILE 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 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 667 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 794 MET Chi-restraints excluded: chain A residue 943 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1275 ASP 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 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 156 ILE 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 352 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain E residue 32 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 E residue 460 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 261 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131683 restraints weight = 38575.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130839 restraints weight = 36411.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132417 restraints weight = 31139.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132482 restraints weight = 20949.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132739 restraints weight = 19276.823| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22950 Z= 0.140 Angle : 0.647 12.895 31054 Z= 0.332 Chirality : 0.045 0.260 3379 Planarity : 0.004 0.051 3928 Dihedral : 6.416 133.391 3121 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.75 % Allowed : 17.89 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2713 helix: 0.43 (0.17), residues: 885 sheet: -1.58 (0.21), residues: 580 loop : -1.86 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 73 TYR 0.035 0.002 TYR F 343 PHE 0.034 0.001 PHE E 384 TRP 0.071 0.002 TRP E 143 HIS 0.007 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (22941) covalent geometry : angle 0.64742 / 0.33 (31054) hydrogen bonds : bond 0.03449 / 2.27 ( 829) hydrogen bonds : angle 4.93358 / 3.42 ( 2376) metal coordination : bond 0.00621 / 0.45 ( 9) ********************** 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 363 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8381 (p0) cc_final: 0.8025 (p0) REVERT: A 80 SER cc_start: 0.9101 (t) cc_final: 0.8734 (m) REVERT: A 469 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 470 LEU cc_start: 0.7872 (tp) cc_final: 0.7413 (mp) REVERT: A 584 MET cc_start: 0.6539 (mtt) cc_final: 0.5995 (mtt) REVERT: A 685 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5116 (m-70) REVERT: A 694 LYS cc_start: 0.7481 (mttt) cc_final: 0.7170 (mmtt) REVERT: A 811 PHE cc_start: 0.7413 (t80) cc_final: 0.6997 (t80) REVERT: A 990 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 1186 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8736 (mt) REVERT: A 1206 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7460 (pp) REVERT: A 1294 MET cc_start: 0.6458 (mmm) cc_final: 0.6249 (mmm) REVERT: B 130 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5322 (mt-10) REVERT: B 229 TRP cc_start: 0.7661 (m100) cc_final: 0.7230 (m100) REVERT: B 292 MET cc_start: 0.8267 (mmm) cc_final: 0.7497 (tpt) REVERT: B 366 GLU cc_start: 0.7646 (pm20) cc_final: 0.7403 (pm20) REVERT: C 93 MET cc_start: 0.4558 (mtp) cc_final: 0.4284 (mmt) REVERT: C 99 TYR cc_start: 0.8106 (t80) cc_final: 0.7872 (t80) REVERT: E 52 LYS cc_start: 0.6898 (pttt) cc_final: 0.6626 (mmtt) REVERT: E 68 TRP cc_start: 0.7000 (m100) cc_final: 0.6695 (t60) REVERT: E 138 MET cc_start: 0.6122 (mmm) cc_final: 0.5762 (mmt) REVERT: E 187 TRP cc_start: 0.5285 (t60) cc_final: 0.4483 (t60) REVERT: E 214 MET cc_start: 0.1001 (tpt) cc_final: 0.0751 (tpt) REVERT: E 542 LYS cc_start: 0.7234 (tttt) cc_final: 0.6852 (tptt) REVERT: F 122 MET cc_start: 0.5073 (tpt) cc_final: 0.4614 (tpp) REVERT: F 303 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7675 (mt0) REVERT: F 487 ARG cc_start: 0.6601 (mmp80) cc_final: 0.6345 (mmp80) outliers start: 66 outliers final: 51 residues processed: 343 average time/residue: 0.1422 time to fit residues: 78.8194 Evaluate side-chains 337 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 535 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 794 MET Chi-restraints excluded: chain A residue 943 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1273 ASP 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 92 LEU 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 156 ILE 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 352 SER Chi-restraints excluded: chain B residue 356 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 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 54 TYR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 530 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 231 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 178 optimal weight: 0.0020 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 159 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 858 GLN ** 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 310 HIS B 325 GLN E 173 GLN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.164121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134367 restraints weight = 38415.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.133780 restraints weight = 34354.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.135140 restraints weight = 27479.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135390 restraints weight = 20298.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135598 restraints weight = 19392.975| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22950 Z= 0.119 Angle : 0.627 12.249 31054 Z= 0.321 Chirality : 0.044 0.233 3379 Planarity : 0.004 0.052 3928 Dihedral : 6.282 132.855 3121 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.50 % Allowed : 18.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2713 helix: 0.51 (0.17), residues: 905 sheet: -1.38 (0.21), residues: 584 loop : -1.91 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 275 TYR 0.030 0.002 TYR F 343 PHE 0.027 0.001 PHE E 384 TRP 0.042 0.002 TRP E 143 HIS 0.024 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (22941) covalent geometry : angle 0.62696 / 0.32 (31054) hydrogen bonds : bond 0.03302 / 2.17 ( 829) hydrogen bonds : angle 4.80203 / 3.33 ( 2376) metal coordination : bond 0.00608 / 0.42 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.39 seconds wall clock time: 63 minutes 39.28 seconds (3819.28 seconds total)