Starting phenix.real_space_refine on Fri Sep 19 02:52:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_20861.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_20861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_20861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_20861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uro_20861/09_2025/6uro_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: {'RNA': 8} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 1} Chain: "E" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4382 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 16, 'TRANS': 510} Chain breaks: 1 Chain: "F" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4382 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 16, 'TRANS': 510} Chain breaks: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12855 SG CYS C 41 68.174 61.972 19.751 1.00 39.96 S ATOM 12954 SG CYS C 55 71.000 59.886 22.804 1.00 39.96 S ATOM 13056 SG CYS C 68 52.178 51.192 23.941 1.00 30.00 S ATOM 13171 SG CYS C 82 55.511 50.824 21.577 1.00 52.97 S ATOM 13292 SG CYS C 96 36.481 48.944 23.117 1.00 39.93 S ATOM 13410 SG CYS C 110 36.082 52.254 24.468 1.00 37.40 S Time building chain proxies: 4.90, per 1000 atoms: 0.22 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: 1.28 Conformation dependent library (CDL) restraints added in 947.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.78 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: 4.98 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4003 1.32 - 1.45: 6042 1.45 - 1.57: 12660 1.57 - 1.70: 15 1.70 - 1.82: 221 Bond restraints: 22941 Sorted by residual: bond pdb=" CG GLN B 73 " pdb=" CD GLN B 73 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB VAL B 111 " pdb=" CG2 VAL B 111 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" N ALA A1250 " pdb=" CA ALA A1250 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.21e+00 bond pdb=" CG LEU B 381 " pdb=" CD2 LEU B 381 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.06e+00 bond pdb=" CB ILE A 945 " pdb=" CG2 ILE A 945 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 ... (remaining 22936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30066 2.61 - 5.21: 865 5.21 - 7.82: 100 7.82 - 10.42: 20 10.42 - 13.03: 3 Bond angle restraints: 31054 Sorted by residual: angle pdb=" N LEU B 386 " pdb=" CA LEU B 386 " pdb=" C LEU B 386 " ideal model delta sigma weight residual 109.96 98.27 11.69 1.50e+00 4.44e-01 6.07e+01 angle pdb=" N ILE A 330 " pdb=" CA ILE A 330 " pdb=" C ILE A 330 " ideal model delta sigma weight residual 110.21 102.15 8.06 1.13e+00 7.83e-01 5.09e+01 angle pdb=" N LEU A 392 " pdb=" CA LEU A 392 " pdb=" C LEU A 392 " ideal model delta sigma weight residual 109.85 120.49 -10.64 1.58e+00 4.01e-01 4.53e+01 angle pdb=" N LEU B 99 " pdb=" CA LEU B 99 " pdb=" C LEU B 99 " ideal model delta sigma weight residual 111.36 104.33 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" C ASP A 333 " ideal model delta sigma weight residual 111.54 120.21 -8.67 1.36e+00 5.41e-01 4.06e+01 ... (remaining 31049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 12904 15.23 - 30.47: 708 30.47 - 45.70: 134 45.70 - 60.94: 26 60.94 - 76.17: 14 Dihedral angle restraints: 13786 sinusoidal: 5729 harmonic: 8057 Sorted by residual: dihedral pdb=" CA SER B 209 " pdb=" C SER B 209 " pdb=" N PHE B 210 " pdb=" CA PHE B 210 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3201 0.114 - 0.228: 167 0.228 - 0.342: 9 0.342 - 0.456: 1 0.456 - 0.570: 1 Chirality restraints: 3379 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA TRP A 256 " pdb=" N TRP A 256 " pdb=" C TRP A 256 " pdb=" CB TRP A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP A1312 " pdb=" N TRP A1312 " pdb=" C TRP A1312 " pdb=" CB TRP A1312 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 3376 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1256 " -0.027 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A1256 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A1256 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A1256 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A1256 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1256 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A1256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1256 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 98 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C MET B 98 " 0.062 2.00e-02 2.50e+03 pdb=" O MET B 98 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 99 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1337 " -0.024 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A1337 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A1337 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A1337 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1337 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1337 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1337 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1337 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1337 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A1337 " 0.001 2.00e-02 2.50e+03 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 319 2.64 - 3.21: 19009 3.21 - 3.77: 34474 3.77 - 4.34: 48773 4.34 - 4.90: 79619 Nonbonded interactions: 182194 Sorted by model distance: nonbonded pdb=" O ASN E 458 " pdb=" ND2 ASN E 458 " model vdw 2.077 3.120 nonbonded pdb=" OE1 GLN A1188 " pdb=" OH TYR B 59 " model vdw 2.250 3.040 nonbonded pdb=" SG CYS A1126 " pdb=" N VAL A1172 " model vdw 2.252 3.480 nonbonded pdb=" OG1 THR A1101 " pdb=" O VAL A1172 " model vdw 2.258 3.040 nonbonded pdb=" OG SER B 221 " pdb=" OD1 ASP B 223 " model vdw 2.264 3.040 ... (remaining 182189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.620 Find NCS groups from input model: 0.310 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.694 22950 Z= 0.412 Angle : 1.053 13.026 31054 Z= 0.613 Chirality : 0.059 0.570 3379 Planarity : 0.007 0.075 3928 Dihedral : 10.427 76.174 8592 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.81 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 aren 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 covalent geometry : bond 0.00857 (22941) covalent geometry : angle 1.05345 (31054) hydrogen bonds : bond 0.29285 ( 829) hydrogen bonds : angle 10.23187 ( 2376) metal coordination : bond 0.27473 ( 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 : 0.605 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: 0.8418 (t) cc_final: 0.7893 (m) REVERT: A 130 ASP cc_start: 0.7616 (t70) cc_final: 0.7391 (t70) REVERT: A 248 THR cc_start: 0.7331 (p) cc_final: 0.7125 (p) REVERT: A 354 MET cc_start: 0.3285 (mmm) cc_final: 0.2782 (mtm) REVERT: A 470 LEU cc_start: 0.8169 (tp) cc_final: 0.7937 (tt) REVERT: A 1186 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (mt) REVERT: A 1206 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7538 (pp) REVERT: A 1247 SER cc_start: 0.8246 (t) cc_final: 0.7840 (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: 0.7061 (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: 0.1784 time to fit residues: 178.9339 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 : 0.862 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 252 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 679 HIS A 680 HIS A 887 ASN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN A1177 HIS ** 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 97 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.168814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135695 restraints weight = 38456.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134401 restraints weight = 28875.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134974 restraints weight = 23627.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135773 restraints weight = 20507.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.137682 restraints weight = 17520.174| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 22950 Z= 0.160 Angle : 0.681 9.982 31054 Z= 0.357 Chirality : 0.045 0.177 3379 Planarity : 0.005 0.049 3928 Dihedral : 6.802 72.964 3143 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.79 % Allowed : 9.82 % Favored : 87.40 % 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 aren not related in a simple way. whole: -3.26 (0.14), residues: 2713 helix: -1.96 (0.14), residues: 892 sheet: -1.77 (0.20), residues: 575 loop : -2.43 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1248 TYR 0.032 0.002 TYR F 71 PHE 0.039 0.002 PHE E 384 TRP 0.030 0.002 TRP E 35 HIS 0.015 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00355 (22941) covalent geometry : angle 0.68149 (31054) hydrogen bonds : bond 0.04743 ( 829) hydrogen bonds : angle 5.90692 ( 2376) metal coordination : bond 0.04383 ( 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: 67 poor density : 445 time to evaluate : 0.818 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: A 24 ASN cc_start: 0.8393 (p0) cc_final: 0.8155 (p0) REVERT: A 80 SER cc_start: 0.8957 (t) cc_final: 0.8637 (m) REVERT: A 470 LEU cc_start: 0.8114 (tp) cc_final: 0.7580 (mp) REVERT: A 953 LEU cc_start: 0.7751 (tp) cc_final: 0.7024 (tt) REVERT: A 998 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8664 (mm) REVERT: A 1206 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7528 (pp) REVERT: B 126 ARG cc_start: 0.7286 (mmp80) cc_final: 0.6994 (mmp80) REVERT: B 273 TRP cc_start: 0.6625 (m100) cc_final: 0.6369 (m100) REVERT: E 28 ASN cc_start: 0.6274 (t0) cc_final: 0.5726 (m-40) REVERT: E 35 TRP cc_start: 0.3293 (m100) cc_final: 0.2830 (m100) REVERT: E 52 LYS cc_start: 0.7328 (pttp) cc_final: 0.6684 (mmtt) REVERT: E 122 MET cc_start: -0.0903 (tpp) cc_final: -0.1442 (tpt) REVERT: E 214 MET cc_start: 0.0874 (tpt) cc_final: 0.0429 (tpt) REVERT: E 227 MET cc_start: 0.5228 (ppp) cc_final: 0.4415 (ttp) REVERT: E 343 TYR cc_start: 0.8009 (m-80) cc_final: 0.6848 (t80) REVERT: E 346 TYR cc_start: 0.7361 (t80) cc_final: 0.6625 (t80) REVERT: E 419 GLU cc_start: 0.6148 (mm-30) cc_final: 0.5942 (mm-30) REVERT: E 460 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6512 (t0) REVERT: E 524 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8178 (tt) REVERT: F 86 LYS cc_start: 0.8865 (mmpt) cc_final: 0.8576 (mtmt) REVERT: F 93 MET cc_start: 0.7736 (mmt) cc_final: 0.7082 (mmt) REVERT: F 122 MET cc_start: 0.4382 (tpp) cc_final: 0.4170 (tpt) REVERT: F 533 LEU cc_start: 0.7542 (mt) cc_final: 0.7246 (mp) REVERT: F 541 LEU cc_start: 0.7110 (mt) cc_final: 0.5850 (pp) outliers start: 67 outliers final: 28 residues processed: 495 average time/residue: 0.1561 time to fit residues: 118.1164 Evaluate side-chains 357 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 685 HIS 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 E residue 460 ASP Chi-restraints excluded: chain E residue 524 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: 7.9990 chunk 257 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 245 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 181 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 325 GLN B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130817 restraints weight = 39155.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129147 restraints weight = 40363.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130447 restraints weight = 37245.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130823 restraints weight = 24574.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130994 restraints weight = 23692.007| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22950 Z= 0.249 Angle : 0.718 12.579 31054 Z= 0.374 Chirality : 0.046 0.173 3379 Planarity : 0.005 0.105 3928 Dihedral : 6.643 72.694 3131 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.16 % Allowed : 13.14 % Favored : 83.69 % 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 aren not related in a simple way. whole: -2.74 (0.15), residues: 2713 helix: -1.02 (0.16), residues: 903 sheet: -1.74 (0.20), residues: 566 loop : -2.42 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 275 TYR 0.028 0.002 TYR E 450 PHE 0.027 0.002 PHE A1074 TRP 0.024 0.002 TRP A1337 HIS 0.014 0.002 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00577 (22941) covalent geometry : angle 0.71771 (31054) hydrogen bonds : bond 0.04372 ( 829) hydrogen bonds : angle 5.62600 ( 2376) metal coordination : bond 0.04239 ( 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 436 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 360 time to evaluate : 0.822 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: A 19 TYR cc_start: 0.8083 (t80) cc_final: 0.7882 (t80) REVERT: A 80 SER cc_start: 0.9141 (t) cc_final: 0.8639 (m) REVERT: A 144 ASP cc_start: 0.6268 (t0) cc_final: 0.5352 (t0) REVERT: A 148 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7137 (mtm-85) REVERT: A 469 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 470 LEU cc_start: 0.8302 (tp) cc_final: 0.7591 (mp) REVERT: A 872 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7408 (pp) REVERT: A 1058 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 1186 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8888 (mt) REVERT: A 1206 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7515 (pp) REVERT: B 99 LEU cc_start: 0.8170 (mt) cc_final: 0.7912 (mt) REVERT: B 411 MET cc_start: 0.7797 (mtm) cc_final: 0.7544 (mtm) REVERT: C 115 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.5760 (tt) REVERT: E 28 ASN cc_start: 0.6462 (t0) cc_final: 0.5710 (m-40) REVERT: E 35 TRP cc_start: 0.3359 (m100) cc_final: 0.3040 (m100) REVERT: E 52 LYS cc_start: 0.6819 (pttp) cc_final: 0.6392 (mmtt) REVERT: E 68 TRP cc_start: 0.7020 (m100) cc_final: 0.6658 (t60) REVERT: E 122 MET cc_start: -0.0195 (tpp) cc_final: -0.0568 (tpp) REVERT: E 138 MET cc_start: 0.5806 (mmm) cc_final: 0.5170 (mmt) REVERT: E 187 TRP cc_start: 0.5006 (t60) cc_final: 0.4136 (t60) REVERT: F 54 TYR cc_start: 0.5341 (m-80) cc_final: 0.4923 (m-80) REVERT: F 71 TYR cc_start: 0.3902 (t80) cc_final: 0.3214 (t80) REVERT: F 84 VAL cc_start: 0.7808 (t) cc_final: 0.7507 (t) REVERT: F 205 MET cc_start: 0.5833 (ttm) cc_final: 0.5284 (ttm) REVERT: F 215 ASN cc_start: 0.6648 (t0) cc_final: 0.5831 (t0) REVERT: F 218 ARG cc_start: 0.4613 (ppt170) cc_final: 0.3239 (mtm-85) REVERT: F 303 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7769 (mt0) REVERT: F 541 LEU cc_start: 0.7190 (mt) cc_final: 0.6102 (pp) outliers start: 76 outliers final: 47 residues processed: 421 average time/residue: 0.1468 time to fit residues: 95.9534 Evaluate side-chains 356 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 375 VAL 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 679 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 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 VAL 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 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 326 ASN Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 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: 1.9990 chunk 78 optimal weight: 0.5980 chunk 178 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 234 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1188 GLN B 69 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 325 GLN B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.163192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131913 restraints weight = 38914.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129835 restraints weight = 32917.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130671 restraints weight = 28876.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131726 restraints weight = 21721.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131803 restraints weight = 18240.142| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22950 Z= 0.149 Angle : 0.620 11.785 31054 Z= 0.322 Chirality : 0.043 0.166 3379 Planarity : 0.004 0.048 3928 Dihedral : 6.233 72.969 3129 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.91 % Allowed : 14.73 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.15), residues: 2713 helix: -0.31 (0.17), residues: 878 sheet: -1.74 (0.20), residues: 598 loop : -2.20 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 627 TYR 0.027 0.002 TYR E 450 PHE 0.031 0.002 PHE B 153 TRP 0.024 0.001 TRP E 258 HIS 0.010 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00345 (22941) covalent geometry : angle 0.62028 (31054) hydrogen bonds : bond 0.03691 ( 829) hydrogen bonds : angle 5.27252 ( 2376) metal coordination : bond 0.00693 ( 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 417 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8418 (p0) cc_final: 0.8036 (p0) REVERT: A 80 SER cc_start: 0.9070 (t) cc_final: 0.8674 (m) REVERT: A 469 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 470 LEU cc_start: 0.8171 (tp) cc_final: 0.7584 (mp) REVERT: A 584 MET cc_start: 0.5643 (mtt) cc_final: 0.5307 (mtt) REVERT: A 685 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5686 (m-70) REVERT: A 872 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7165 (pp) REVERT: A 1058 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 1206 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7433 (pp) REVERT: A 1342 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: B 103 MET cc_start: 0.7775 (mmt) cc_final: 0.7449 (mmt) REVERT: B 229 TRP cc_start: 0.7329 (m100) cc_final: 0.7085 (m100) REVERT: B 411 MET cc_start: 0.7762 (mtm) cc_final: 0.7471 (mtm) REVERT: C 69 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6082 (ttpt) REVERT: C 115 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.5918 (tt) REVERT: E 35 TRP cc_start: 0.3256 (m100) cc_final: 0.3016 (m100) REVERT: E 122 MET cc_start: -0.0855 (tpp) cc_final: -0.1152 (tpp) REVERT: E 138 MET cc_start: 0.6089 (mmm) cc_final: 0.5683 (mmm) REVERT: E 187 TRP cc_start: 0.5456 (t60) cc_final: 0.4552 (t60) REVERT: E 214 MET cc_start: 0.0806 (tpt) cc_final: 0.0371 (tpt) REVERT: E 274 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7487 (mmtt) REVERT: E 300 TYR cc_start: 0.7392 (t80) cc_final: 0.7163 (t80) REVERT: F 54 TYR cc_start: 0.6318 (m-80) cc_final: 0.5469 (m-80) REVERT: F 67 PHE cc_start: 0.6813 (m-80) cc_final: 0.6574 (m-80) REVERT: F 71 TYR cc_start: 0.4127 (t80) cc_final: 0.3148 (t80) REVERT: F 138 MET cc_start: 0.6458 (tpp) cc_final: 0.6250 (mmt) REVERT: F 205 MET cc_start: 0.5497 (ttm) cc_final: 0.5059 (ttm) REVERT: F 215 ASN cc_start: 0.6859 (t0) cc_final: 0.5905 (t0) REVERT: F 218 ARG cc_start: 0.4353 (ppt170) cc_final: 0.3010 (mtm-85) REVERT: F 303 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7808 (mt0) REVERT: F 457 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7114 (mm) REVERT: F 541 LEU cc_start: 0.7570 (mt) cc_final: 0.6369 (pp) outliers start: 70 outliers final: 38 residues processed: 402 average time/residue: 0.1404 time to fit residues: 88.6708 Evaluate side-chains 348 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 657 VAL Chi-restraints excluded: chain A residue 659 MET 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 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 1206 ILE Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1342 ASP 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 151 PHE Chi-restraints excluded: chain B residue 172 ASN 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 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 336 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 236 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 458 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.158617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127798 restraints weight = 38992.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125875 restraints weight = 40100.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127198 restraints weight = 36766.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127731 restraints weight = 26564.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128105 restraints weight = 23431.730| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22950 Z= 0.221 Angle : 0.672 13.099 31054 Z= 0.350 Chirality : 0.045 0.168 3379 Planarity : 0.005 0.050 3928 Dihedral : 6.330 72.779 3129 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.54 % Allowed : 14.68 % Favored : 81.78 % 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 aren not related in a simple way. whole: -2.13 (0.15), residues: 2713 helix: -0.09 (0.17), residues: 898 sheet: -1.80 (0.20), residues: 595 loop : -2.20 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 90 TYR 0.031 0.002 TYR E 450 PHE 0.034 0.002 PHE A1074 TRP 0.027 0.002 TRP E 258 HIS 0.026 0.002 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00514 (22941) covalent geometry : angle 0.67230 (31054) hydrogen bonds : bond 0.03892 ( 829) hydrogen bonds : angle 5.29473 ( 2376) metal coordination : bond 0.01350 ( 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 413 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 328 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9135 (t) cc_final: 0.8691 (m) REVERT: A 469 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8238 (mt) REVERT: A 470 LEU cc_start: 0.8302 (tp) cc_final: 0.7639 (mp) REVERT: A 584 MET cc_start: 0.6060 (mtt) cc_final: 0.5633 (mtt) REVERT: A 685 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5625 (m-70) REVERT: A 694 LYS cc_start: 0.7542 (mttt) cc_final: 0.7232 (mmtt) REVERT: A 872 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7255 (pp) REVERT: A 1058 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 1186 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8813 (mt) REVERT: A 1206 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7641 (pp) REVERT: B 367 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7994 (m) REVERT: B 411 MET cc_start: 0.7778 (mtm) cc_final: 0.7496 (mtm) REVERT: C 70 HIS cc_start: 0.6430 (m170) cc_final: 0.6086 (m170) REVERT: C 115 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5954 (tt) REVERT: E 28 ASN cc_start: 0.5514 (t0) cc_final: 0.5238 (p0) REVERT: E 52 LYS cc_start: 0.7071 (pttt) cc_final: 0.6610 (mmtt) REVERT: E 68 TRP cc_start: 0.7168 (m100) cc_final: 0.6756 (t60) REVERT: E 187 TRP cc_start: 0.5102 (t60) cc_final: 0.4325 (t60) REVERT: E 524 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8221 (tt) REVERT: E 542 LYS cc_start: 0.7009 (tttt) cc_final: 0.6643 (tptt) REVERT: F 67 PHE cc_start: 0.6635 (m-80) cc_final: 0.6429 (m-80) REVERT: F 93 MET cc_start: 0.8109 (mmt) cc_final: 0.7685 (mmt) REVERT: F 205 MET cc_start: 0.5632 (ttm) cc_final: 0.5225 (ttm) REVERT: F 303 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7768 (mt0) REVERT: F 314 MET cc_start: 0.6490 (tpp) cc_final: 0.6264 (ttt) REVERT: F 541 LEU cc_start: 0.7574 (mt) cc_final: 0.6421 (pp) outliers start: 85 outliers final: 51 residues processed: 393 average time/residue: 0.1403 time to fit residues: 87.3802 Evaluate side-chains 346 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 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 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 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain 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 124 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 93 MET 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 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 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.159245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128054 restraints weight = 39268.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127057 restraints weight = 32912.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128343 restraints weight = 25829.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129129 restraints weight = 19394.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129275 restraints weight = 18407.459| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22950 Z= 0.175 Angle : 0.636 12.226 31054 Z= 0.330 Chirality : 0.044 0.175 3379 Planarity : 0.004 0.049 3928 Dihedral : 6.200 72.924 3129 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.70 % Allowed : 15.72 % Favored : 80.57 % 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 aren not related in a simple way. whole: -1.99 (0.16), residues: 2713 helix: 0.06 (0.17), residues: 881 sheet: -1.82 (0.20), residues: 603 loop : -2.05 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 90 TYR 0.042 0.002 TYR F 346 PHE 0.041 0.002 PHE B 153 TRP 0.054 0.002 TRP E 35 HIS 0.008 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00409 (22941) covalent geometry : angle 0.63608 (31054) hydrogen bonds : bond 0.03640 ( 829) hydrogen bonds : angle 5.17816 ( 2376) metal coordination : bond 0.01097 ( 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 403 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 314 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9093 (t) cc_final: 0.8666 (m) REVERT: A 469 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 470 LEU cc_start: 0.8130 (tp) cc_final: 0.7514 (mp) REVERT: A 584 MET cc_start: 0.6081 (mtt) cc_final: 0.5600 (mtt) REVERT: A 685 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5637 (m-70) REVERT: A 694 LYS cc_start: 0.7562 (mttt) cc_final: 0.7152 (mmtt) REVERT: A 1186 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 1206 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7542 (pp) REVERT: B 103 MET cc_start: 0.7890 (mmt) cc_final: 0.7636 (mmt) REVERT: B 292 MET cc_start: 0.8277 (mmm) cc_final: 0.7600 (tpt) REVERT: B 367 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7704 (m) REVERT: C 70 HIS cc_start: 0.6522 (m170) cc_final: 0.6232 (m170) REVERT: C 115 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5960 (tt) REVERT: E 28 ASN cc_start: 0.5879 (t0) cc_final: 0.5344 (p0) REVERT: E 52 LYS cc_start: 0.7077 (pttt) cc_final: 0.6684 (mptt) REVERT: E 68 TRP cc_start: 0.7256 (m100) cc_final: 0.6817 (t60) REVERT: E 122 MET cc_start: -0.0132 (tpp) cc_final: -0.0522 (tpp) REVERT: E 136 GLU cc_start: 0.5518 (tp30) cc_final: 0.5047 (tp30) REVERT: E 138 MET cc_start: 0.6201 (mmm) cc_final: 0.3725 (mtt) REVERT: E 187 TRP cc_start: 0.5187 (t60) cc_final: 0.4382 (t60) REVERT: E 214 MET cc_start: 0.1003 (tpt) cc_final: 0.0622 (tpt) REVERT: E 524 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 542 LYS cc_start: 0.7182 (tttt) cc_final: 0.6811 (tptt) REVERT: F 54 TYR cc_start: 0.6155 (m-80) cc_final: 0.5723 (t80) REVERT: F 67 PHE cc_start: 0.6579 (m-80) cc_final: 0.6127 (m-80) REVERT: F 71 TYR cc_start: 0.4294 (t80) cc_final: 0.3080 (t80) REVERT: F 187 TRP cc_start: 0.4994 (t-100) cc_final: 0.4704 (m-90) REVERT: F 205 MET cc_start: 0.5520 (ttm) cc_final: 0.5135 (ttm) REVERT: F 303 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7801 (mt0) REVERT: F 314 MET cc_start: 0.6473 (tpp) cc_final: 0.6081 (ttm) REVERT: F 327 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7597 (mt) REVERT: F 541 LEU cc_start: 0.7545 (mt) cc_final: 0.6365 (pp) outliers start: 89 outliers final: 60 residues processed: 384 average time/residue: 0.1361 time to fit residues: 84.6251 Evaluate side-chains 356 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 612 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 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 782 THR 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 1210 LEU Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain 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 124 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 93 MET 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 336 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 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 327 ILE Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 457 LEU 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN C 26 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.159695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128064 restraints weight = 39073.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126310 restraints weight = 32950.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127642 restraints weight = 26980.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128340 restraints weight = 19093.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128413 restraints weight = 17216.094| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22950 Z= 0.158 Angle : 0.639 11.519 31054 Z= 0.328 Chirality : 0.044 0.175 3379 Planarity : 0.004 0.048 3928 Dihedral : 6.121 72.999 3129 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.74 % Allowed : 16.22 % Favored : 80.03 % 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 aren not related in a simple way. whole: -1.87 (0.16), residues: 2713 helix: 0.18 (0.17), residues: 882 sheet: -1.73 (0.20), residues: 601 loop : -2.01 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.039 0.002 TYR E 450 PHE 0.026 0.002 PHE B 210 TRP 0.041 0.002 TRP E 35 HIS 0.007 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00369 (22941) covalent geometry : angle 0.63867 (31054) hydrogen bonds : bond 0.03562 ( 829) hydrogen bonds : angle 5.05842 ( 2376) metal coordination : bond 0.01273 ( 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 412 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 322 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8515 (p0) cc_final: 0.8092 (p0) REVERT: A 80 SER cc_start: 0.9109 (t) cc_final: 0.8680 (m) REVERT: A 469 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8029 (mt) REVERT: A 470 LEU cc_start: 0.8060 (tp) cc_final: 0.7462 (mp) REVERT: A 584 MET cc_start: 0.6143 (mtt) cc_final: 0.5626 (mtt) REVERT: A 679 HIS cc_start: 0.5206 (OUTLIER) cc_final: 0.4907 (m-70) REVERT: A 685 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5615 (m-70) REVERT: A 694 LYS cc_start: 0.7599 (mttt) cc_final: 0.7125 (mmtt) REVERT: A 1206 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7561 (pp) REVERT: B 130 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5643 (mt-10) REVERT: B 292 MET cc_start: 0.8280 (mmm) cc_final: 0.7562 (tpt) REVERT: C 70 HIS cc_start: 0.6567 (m170) cc_final: 0.6272 (m170) REVERT: C 115 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6151 (tt) REVERT: E 28 ASN cc_start: 0.5942 (t0) cc_final: 0.5347 (p0) REVERT: E 35 TRP cc_start: 0.3206 (m100) cc_final: 0.2721 (m100) REVERT: E 52 LYS cc_start: 0.7128 (pttt) cc_final: 0.6678 (mmtt) REVERT: E 68 TRP cc_start: 0.7269 (m100) cc_final: 0.6764 (t60) REVERT: E 122 MET cc_start: -0.0345 (tpp) cc_final: -0.0669 (tpp) REVERT: E 187 TRP cc_start: 0.5356 (t60) cc_final: 0.4538 (t60) REVERT: E 214 MET cc_start: 0.1217 (tpt) cc_final: 0.0903 (tpt) REVERT: E 330 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7788 (ttp-170) REVERT: E 524 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (tt) REVERT: E 542 LYS cc_start: 0.7331 (tttt) cc_final: 0.6872 (tptt) REVERT: F 54 TYR cc_start: 0.6529 (m-80) cc_final: 0.5900 (t80) REVERT: F 67 PHE cc_start: 0.6545 (m-80) cc_final: 0.6087 (m-80) REVERT: F 71 TYR cc_start: 0.4414 (t80) cc_final: 0.3164 (t80) REVERT: F 303 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7871 (mt0) REVERT: F 314 MET cc_start: 0.6488 (tpp) cc_final: 0.6159 (ttm) REVERT: F 327 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7547 (mt) REVERT: F 354 MET cc_start: 0.7436 (mmm) cc_final: 0.6664 (mtm) outliers start: 90 outliers final: 61 residues processed: 391 average time/residue: 0.1286 time to fit residues: 81.2237 Evaluate side-chains 362 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 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 998 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 122 VAL 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 177 LEU 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 386 LEU 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 336 LEU 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 327 ILE Chi-restraints excluded: chain F residue 328 TYR Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 187 optimal weight: 0.0040 chunk 269 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 HIS ** 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.163292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133000 restraints weight = 38559.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132115 restraints weight = 37015.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133925 restraints weight = 27415.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134591 restraints weight = 18463.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134915 restraints weight = 18047.012| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22950 Z= 0.119 Angle : 0.631 13.853 31054 Z= 0.317 Chirality : 0.043 0.166 3379 Planarity : 0.004 0.050 3928 Dihedral : 5.901 73.210 3129 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.75 % Allowed : 17.14 % Favored : 80.12 % 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 aren not related in a simple way. whole: -1.64 (0.16), residues: 2713 helix: 0.36 (0.17), residues: 894 sheet: -1.56 (0.21), residues: 585 loop : -1.91 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 40 TYR 0.037 0.002 TYR E 450 PHE 0.021 0.001 PHE F 530 TRP 0.045 0.002 TRP F 187 HIS 0.006 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00274 (22941) covalent geometry : angle 0.63105 (31054) hydrogen bonds : bond 0.03315 ( 829) hydrogen bonds : angle 4.92620 ( 2376) metal coordination : bond 0.00837 ( 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 400 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8350 (p0) cc_final: 0.8005 (p0) REVERT: A 80 SER cc_start: 0.8957 (t) cc_final: 0.8655 (m) REVERT: A 249 GLN cc_start: 0.8050 (mm110) cc_final: 0.7771 (mp10) REVERT: A 470 LEU cc_start: 0.7897 (tp) cc_final: 0.7485 (mp) REVERT: A 584 MET cc_start: 0.6280 (mtt) cc_final: 0.5806 (mtt) REVERT: A 685 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.5371 (m-70) REVERT: A 694 LYS cc_start: 0.7411 (mttt) cc_final: 0.6957 (mmtm) REVERT: A 1186 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 1206 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7669 (pp) REVERT: A 1383 MET cc_start: 0.7318 (mmm) cc_final: 0.7095 (mmm) REVERT: B 126 ARG cc_start: 0.6989 (mmp80) cc_final: 0.6729 (mmp80) REVERT: B 292 MET cc_start: 0.8219 (mmm) cc_final: 0.7458 (tpt) REVERT: C 70 HIS cc_start: 0.6336 (m170) cc_final: 0.6045 (m170) REVERT: E 28 ASN cc_start: 0.6046 (t0) cc_final: 0.5503 (p0) REVERT: E 35 TRP cc_start: 0.3370 (m100) cc_final: 0.3016 (m100) REVERT: E 52 LYS cc_start: 0.6995 (pttt) cc_final: 0.6702 (mmtt) REVERT: E 90 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.6442 (ptm160) REVERT: E 122 MET cc_start: -0.0164 (tpp) cc_final: -0.0524 (tpp) REVERT: E 135 MET cc_start: 0.4155 (ptm) cc_final: 0.3884 (mmt) REVERT: E 138 MET cc_start: 0.6445 (mmm) cc_final: 0.3876 (mtt) REVERT: E 187 TRP cc_start: 0.4862 (t60) cc_final: 0.4244 (t60) REVERT: E 300 TYR cc_start: 0.6701 (t80) cc_final: 0.6468 (t80) REVERT: E 319 LEU cc_start: 0.7822 (tt) cc_final: 0.7475 (tp) REVERT: E 343 TYR cc_start: 0.7777 (m-80) cc_final: 0.6840 (t80) REVERT: E 408 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7150 (ptt180) REVERT: E 542 LYS cc_start: 0.7205 (tttt) cc_final: 0.6867 (tptt) REVERT: F 54 TYR cc_start: 0.5944 (m-80) cc_final: 0.5731 (t80) REVERT: F 67 PHE cc_start: 0.6333 (m-80) cc_final: 0.5788 (m-80) REVERT: F 71 TYR cc_start: 0.4158 (t80) cc_final: 0.3082 (t80) REVERT: F 138 MET cc_start: 0.6590 (tmm) cc_final: 0.6264 (tmm) REVERT: F 327 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (mt) REVERT: F 354 MET cc_start: 0.7291 (mmm) cc_final: 0.6630 (mtm) outliers start: 66 outliers final: 52 residues processed: 381 average time/residue: 0.1327 time to fit residues: 81.4810 Evaluate side-chains 366 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 310 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 THR 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 782 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 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 1309 ASN Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain F residue 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 133 ILE 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 327 ILE Chi-restraints excluded: chain F residue 328 TYR 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: 8.9990 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 157 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 30.0000 chunk 233 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 679 HIS ** A 858 GLN ** 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** E 45 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.158448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.128343 restraints weight = 39194.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126808 restraints weight = 38893.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128443 restraints weight = 32842.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128595 restraints weight = 22815.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128835 restraints weight = 21069.989| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22950 Z= 0.215 Angle : 0.705 14.140 31054 Z= 0.358 Chirality : 0.046 0.188 3379 Planarity : 0.004 0.053 3928 Dihedral : 6.130 72.919 3129 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.79 % Allowed : 17.72 % 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 aren not related in a simple way. whole: -1.69 (0.16), residues: 2713 helix: 0.34 (0.17), residues: 889 sheet: -1.66 (0.20), residues: 590 loop : -1.92 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 40 TYR 0.052 0.002 TYR E 280 PHE 0.036 0.002 PHE A1074 TRP 0.070 0.003 TRP E 143 HIS 0.014 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00508 (22941) covalent geometry : angle 0.70471 (31054) hydrogen bonds : bond 0.03697 ( 829) hydrogen bonds : angle 5.10618 ( 2376) metal coordination : bond 0.00930 ( 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 374 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9151 (t) cc_final: 0.8716 (m) REVERT: A 249 GLN cc_start: 0.8190 (mm110) cc_final: 0.7742 (mp10) REVERT: A 469 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 470 LEU cc_start: 0.8112 (tp) cc_final: 0.7496 (mp) REVERT: A 584 MET cc_start: 0.6471 (mtt) cc_final: 0.5936 (mtt) REVERT: A 694 LYS cc_start: 0.7652 (mttt) cc_final: 0.7220 (mmtt) REVERT: A 811 PHE cc_start: 0.7559 (t80) cc_final: 0.7039 (t80) REVERT: A 1186 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8827 (mt) REVERT: A 1206 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 130 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5533 (mt-10) REVERT: B 181 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.5875 (t70) REVERT: B 292 MET cc_start: 0.8309 (mmm) cc_final: 0.7615 (tpt) REVERT: E 28 ASN cc_start: 0.6071 (t0) cc_final: 0.5327 (p0) REVERT: E 35 TRP cc_start: 0.3306 (m100) cc_final: 0.3072 (m100) REVERT: E 52 LYS cc_start: 0.7016 (pttt) cc_final: 0.6697 (mmtt) REVERT: E 68 TRP cc_start: 0.7042 (m100) cc_final: 0.6583 (t60) REVERT: E 138 MET cc_start: 0.6454 (mmm) cc_final: 0.4155 (mtt) REVERT: E 187 TRP cc_start: 0.4942 (t60) cc_final: 0.4304 (t60) REVERT: E 274 LYS cc_start: 0.7739 (tmtt) cc_final: 0.7524 (mmtt) REVERT: E 405 THR cc_start: 0.6047 (OUTLIER) cc_final: 0.5631 (m) REVERT: E 524 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7500 (tt) REVERT: E 542 LYS cc_start: 0.7307 (tttt) cc_final: 0.6874 (tptt) REVERT: F 67 PHE cc_start: 0.6478 (m-80) cc_final: 0.5913 (m-80) outliers start: 67 outliers final: 53 residues processed: 363 average time/residue: 0.1336 time to fit residues: 77.9069 Evaluate side-chains 351 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 291 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 794 MET 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 1100 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 105 CYS 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 57 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 133 ILE 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 327 ILE Chi-restraints excluded: chain F residue 328 TYR 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: 5.9990 chunk 192 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.161855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131766 restraints weight = 38810.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130333 restraints weight = 37084.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131746 restraints weight = 30072.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132419 restraints weight = 21294.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132466 restraints weight = 19928.874| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22950 Z= 0.131 Angle : 0.661 12.808 31054 Z= 0.333 Chirality : 0.044 0.209 3379 Planarity : 0.004 0.053 3928 Dihedral : 5.970 73.324 3129 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.29 % Allowed : 18.47 % Favored : 79.24 % 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 aren not related in a simple way. whole: -1.58 (0.16), residues: 2713 helix: 0.46 (0.17), residues: 889 sheet: -1.51 (0.21), residues: 584 loop : -1.92 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 40 TYR 0.053 0.002 TYR F 378 PHE 0.031 0.002 PHE A1074 TRP 0.048 0.002 TRP B 229 HIS 0.010 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00307 (22941) covalent geometry : angle 0.66067 (31054) hydrogen bonds : bond 0.03382 ( 829) hydrogen bonds : angle 4.97678 ( 2376) metal coordination : bond 0.00736 ( 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 367 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 312 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8383 (p0) cc_final: 0.8006 (p0) REVERT: A 80 SER cc_start: 0.9033 (t) cc_final: 0.8685 (m) REVERT: A 469 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 470 LEU cc_start: 0.7916 (tp) cc_final: 0.7465 (mp) REVERT: A 584 MET cc_start: 0.6497 (mtm) cc_final: 0.5938 (mtt) REVERT: A 694 LYS cc_start: 0.7495 (mttt) cc_final: 0.7175 (mmtt) REVERT: A 784 TRP cc_start: 0.7521 (m100) cc_final: 0.6942 (m100) REVERT: A 811 PHE cc_start: 0.7404 (t80) cc_final: 0.7011 (t80) REVERT: A 1186 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8766 (mt) REVERT: A 1206 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7696 (pp) REVERT: B 130 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5360 (mt-10) REVERT: B 273 TRP cc_start: 0.7239 (m100) cc_final: 0.6963 (m100) REVERT: B 292 MET cc_start: 0.8171 (mmm) cc_final: 0.7453 (tpt) REVERT: E 28 ASN cc_start: 0.6041 (t0) cc_final: 0.5460 (p0) REVERT: E 52 LYS cc_start: 0.7029 (pttt) cc_final: 0.6686 (mmtt) REVERT: E 68 TRP cc_start: 0.6951 (m100) cc_final: 0.6620 (t60) REVERT: E 138 MET cc_start: 0.6402 (mmm) cc_final: 0.4144 (mtt) REVERT: E 214 MET cc_start: 0.1124 (tpt) cc_final: 0.0801 (tpt) REVERT: E 274 LYS cc_start: 0.7927 (tmtt) cc_final: 0.7386 (mmtt) REVERT: E 542 LYS cc_start: 0.7223 (tttt) cc_final: 0.6830 (tptt) REVERT: F 67 PHE cc_start: 0.6096 (m-80) cc_final: 0.5860 (m-80) REVERT: F 71 TYR cc_start: 0.4084 (t80) cc_final: 0.3678 (t80) REVERT: F 215 ASN cc_start: 0.6102 (t0) cc_final: 0.5525 (p0) REVERT: F 327 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7667 (mt) REVERT: F 354 MET cc_start: 0.6869 (mmm) cc_final: 0.6450 (mtm) REVERT: F 487 ARG cc_start: 0.6594 (mmp80) cc_final: 0.6371 (mmp80) outliers start: 55 outliers final: 45 residues processed: 356 average time/residue: 0.1297 time to fit residues: 74.6868 Evaluate side-chains 346 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 794 MET 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 1186 ILE Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 356 LEU 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 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 133 ILE 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 327 ILE Chi-restraints excluded: chain F residue 328 TYR Chi-restraints excluded: chain F residue 403 GLU Chi-restraints excluded: chain F residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 231 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 178 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 174 optimal weight: 30.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN A1303 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127435 restraints weight = 39213.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125981 restraints weight = 37135.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127414 restraints weight = 31901.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127733 restraints weight = 22183.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127888 restraints weight = 21793.519| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22950 Z= 0.214 Angle : 0.714 13.484 31054 Z= 0.363 Chirality : 0.046 0.183 3379 Planarity : 0.004 0.056 3928 Dihedral : 6.168 73.054 3129 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.75 % Allowed : 18.01 % Favored : 79.24 % 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 aren not related in a simple way. whole: -1.65 (0.16), residues: 2713 helix: 0.40 (0.17), residues: 888 sheet: -1.66 (0.20), residues: 599 loop : -1.90 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 40 TYR 0.041 0.002 TYR F 378 PHE 0.026 0.002 PHE F 530 TRP 0.066 0.003 TRP E 143 HIS 0.009 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00505 (22941) covalent geometry : angle 0.71397 (31054) hydrogen bonds : bond 0.03660 ( 829) hydrogen bonds : angle 5.10635 ( 2376) metal coordination : bond 0.00968 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.64 seconds wall clock time: 60 minutes 15.76 seconds (3615.76 seconds total)