Starting phenix.real_space_refine on Thu Feb 5 13:54:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527.map" model { file = "/net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpd_74527/02_2026/9zpd_74527_neut.cif" } resolution = 3.38 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= 0.016 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 1 6.06 5 P 3 5.49 5 S 94 5.16 5 C 11069 2.51 5 N 3022 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17403 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8642 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 51, 'TRANS': 1029} Chain breaks: 7 Chain: "B" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2034 Classifications: {'peptide': 250} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 236} Chain breaks: 2 Chain: "C" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3384 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 12, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3094 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 368} Chain breaks: 2 Chain: "E" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 216 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14147 SG CYS D 21 19.579 96.755 38.388 1.00125.77 S ATOM 14591 SG CYS D 137 19.255 99.801 36.698 1.00125.09 S ATOM 14615 SG CYS D 140 22.719 100.051 39.583 1.00132.65 S Time building chain proxies: 3.92, per 1000 atoms: 0.23 Number of scatterers: 17403 At special positions: 0 Unit cell: (86.48, 150.4, 240.64, 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 1 29.99 S 94 16.00 P 3 15.00 O 3214 8.00 N 3022 7.00 C 11069 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: 1.66 Conformation dependent library (CDL) restraints added in 808.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 140 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 137 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 21 " 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4094 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 50.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.791A pdb=" N SER A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.506A pdb=" N SER A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.526A pdb=" N ASP A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.187A pdb=" N TYR A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.654A pdb=" N LYS A 333 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU A 334 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 336 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 337 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 374 through 387 removed outlier: 3.615A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.766A pdb=" N HIS A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.631A pdb=" N ILE A 456 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 475 through 503 removed outlier: 3.690A pdb=" N ARG A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 546 removed outlier: 3.577A pdb=" N SER A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 4.316A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 583 through 587 removed outlier: 3.547A pdb=" N ASN A 586 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 609 removed outlier: 3.969A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 628 through 645 removed outlier: 3.649A pdb=" N ILE A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 4.027A pdb=" N VAL A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.767A pdb=" N LEU A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 737 through 753 Processing helix chain 'A' and resid 764 through 777 Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 790 through 804 Processing helix chain 'A' and resid 940 through 968 removed outlier: 3.531A pdb=" N ALA A 968 " --> pdb=" O MET A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1276 removed outlier: 3.628A pdb=" N SER A1276 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 removed outlier: 4.020A pdb=" N VAL B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.539A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 212 removed outlier: 3.968A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 192 through 324 removed outlier: 3.799A pdb=" N THR C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.591A pdb=" N GLN C 353 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 379 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 418 through 440 removed outlier: 3.807A pdb=" N HIS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 461 removed outlier: 3.841A pdb=" N ASN C 453 " --> pdb=" O GLN C 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 removed outlier: 3.792A pdb=" N LYS D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 137 through 172 Processing helix chain 'D' and resid 176 through 265 removed outlier: 3.665A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 299 through 322 Processing helix chain 'D' and resid 362 through 387 removed outlier: 4.136A pdb=" N ASP D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 447 removed outlier: 3.513A pdb=" N PHE D 447 " --> pdb=" O VAL D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.847A pdb=" N VAL A 50 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 48 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 996 through 1002 removed outlier: 4.614A pdb=" N ARG A 998 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS A1011 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A1008 " --> pdb=" O TRP A1020 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1048 through 1050 Processing sheet with id=AA5, first strand: chain 'A' and resid 1048 through 1050 Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 6.924A pdb=" N GLY A1123 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1130 " --> pdb=" O ASP A1125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 3.678A pdb=" N SER A1146 " --> pdb=" O GLY A1159 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET A1165 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A1178 " --> pdb=" O MET A1165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1199 through 1201 removed outlier: 6.498A pdb=" N MET A1212 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A1299 " --> pdb=" O ARG A1221 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1242 through 1248 removed outlier: 4.010A pdb=" N GLY A1244 " --> pdb=" O ALA A1259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1288 through 1290 Processing sheet with id=AB2, first strand: chain 'A' and resid 1332 through 1336 removed outlier: 6.773A pdb=" N ALA A1348 " --> pdb=" O THR A1333 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A1335 " --> pdb=" O VAL A1346 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A1346 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A1345 " --> pdb=" O TRP A1357 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A1355 " --> pdb=" O THR A1347 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 96 removed outlier: 7.285A pdb=" N TRP B 87 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER B 25 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 89 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 19 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N MET B 218 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU B 26 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR B 216 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET B 215 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 145 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.674A pdb=" N TYR B 58 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.674A pdb=" N TYR B 58 " --> pdb=" O TRP B 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 51 removed outlier: 4.031A pdb=" N TYR C 161 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 76 through 79 removed outlier: 5.814A pdb=" N LYS C 78 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 70 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS C 71 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS C 112 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE C 113 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS C 132 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 115 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 130 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 117 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.525A pdb=" N ARG C 188 " --> pdb=" O LYS D 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'C' and resid 386 through 387 removed outlier: 3.720A pdb=" N THR C 394 " --> pdb=" O ILE C 387 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 276 through 278 removed outlier: 4.382A pdb=" N GLY D 283 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 328 through 331 removed outlier: 3.552A pdb=" N ARG D 329 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 349 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 395 through 397 removed outlier: 3.749A pdb=" N ARG D 395 " --> pdb=" O GLU D 404 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2655 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: 3.24 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3735 1.33 - 1.45: 3874 1.45 - 1.57: 10003 1.57 - 1.70: 5 1.70 - 1.82: 143 Bond restraints: 17760 Sorted by residual: bond pdb=" N LEU D 136 " pdb=" CA LEU D 136 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.83e+00 bond pdb=" N ILE A 561 " pdb=" CA ILE A 561 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.62e+00 bond pdb=" N VAL A1210 " pdb=" CA VAL A1210 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.38e+00 bond pdb=" N GLU A 969 " pdb=" CA GLU A 969 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.07e+00 bond pdb=" N ASP B 227 " pdb=" CA ASP B 227 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.03e+00 ... (remaining 17755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 23448 1.98 - 3.95: 495 3.95 - 5.93: 48 5.93 - 7.90: 3 7.90 - 9.88: 4 Bond angle restraints: 23998 Sorted by residual: angle pdb=" C ALA A1250 " pdb=" CA ALA A1250 " pdb=" CB ALA A1250 " ideal model delta sigma weight residual 116.54 111.10 5.44 1.15e+00 7.56e-01 2.23e+01 angle pdb=" N PRO A1237 " pdb=" CA PRO A1237 " pdb=" C PRO A1237 " ideal model delta sigma weight residual 114.75 122.53 -7.78 1.70e+00 3.46e-01 2.09e+01 angle pdb=" N ARG A 237 " pdb=" CA ARG A 237 " pdb=" C ARG A 237 " ideal model delta sigma weight residual 111.28 106.84 4.44 1.09e+00 8.42e-01 1.66e+01 angle pdb=" CA LEU A 984 " pdb=" C LEU A 984 " pdb=" O LEU A 984 " ideal model delta sigma weight residual 121.56 117.21 4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N PRO A 977 " pdb=" CA PRO A 977 " pdb=" C PRO A 977 " ideal model delta sigma weight residual 114.98 109.24 5.74 1.46e+00 4.69e-01 1.55e+01 ... (remaining 23993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 9971 22.21 - 44.42: 700 44.42 - 66.63: 88 66.63 - 88.84: 18 88.84 - 111.05: 4 Dihedral angle restraints: 10781 sinusoidal: 4482 harmonic: 6299 Sorted by residual: dihedral pdb=" C4' GTP A1501 " pdb=" C5' GTP A1501 " pdb=" O5' GTP A1501 " pdb=" PA GTP A1501 " ideal model delta sinusoidal sigma weight residual 260.87 149.82 111.05 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C8 GTP A1501 " pdb=" C1' GTP A1501 " pdb=" N9 GTP A1501 " pdb=" O4' GTP A1501 " ideal model delta sinusoidal sigma weight residual 104.59 12.00 92.59 1 2.00e+01 2.50e-03 2.51e+01 ... (remaining 10778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 2653 0.335 - 0.670: 8 0.670 - 1.005: 0 1.005 - 1.340: 0 1.340 - 1.676: 2 Chirality restraints: 2663 Sorted by residual: chirality pdb=" CG LEU B 91 " pdb=" CB LEU B 91 " pdb=" CD1 LEU B 91 " pdb=" CD2 LEU B 91 " both_signs ideal model delta sigma weight residual False -2.59 -0.91 -1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" CG LEU C 321 " pdb=" CB LEU C 321 " pdb=" CD1 LEU C 321 " pdb=" CD2 LEU C 321 " both_signs ideal model delta sigma weight residual False -2.59 -0.95 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" CB VAL C 33 " pdb=" CA VAL C 33 " pdb=" CG1 VAL C 33 " pdb=" CG2 VAL C 33 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.82e+00 ... (remaining 2660 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 561 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C ILE A 561 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE A 561 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A 562 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 105 " -0.183 9.50e-02 1.11e+02 8.22e-02 4.15e+00 pdb=" NE ARG C 105 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 105 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 105 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 105 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 565 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C CYS A 565 " -0.031 2.00e-02 2.50e+03 pdb=" O CYS A 565 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 566 " 0.011 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 662 2.72 - 3.27: 17931 3.27 - 3.81: 27317 3.81 - 4.36: 33077 4.36 - 4.90: 56646 Nonbonded interactions: 135633 Sorted by model distance: nonbonded pdb=" O LEU C 97 " pdb=" CD1 LEU C 97 " model vdw 2.177 3.460 nonbonded pdb=" OD1 ASP A 428 " pdb=" N SER A 429 " model vdw 2.199 3.120 nonbonded pdb=" O SER A1039 " pdb=" OG SER A1039 " model vdw 2.293 3.040 nonbonded pdb=" CG2 VAL A 52 " pdb=" CE1 PHE A 102 " model vdw 2.295 3.760 nonbonded pdb=" OE1 GLU A 303 " pdb=" OE2 GLU A 305 " model vdw 2.358 3.040 ... (remaining 135628 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.567 17763 Z= 0.321 Angle : 0.638 9.881 23998 Z= 0.390 Chirality : 0.066 1.676 2663 Planarity : 0.004 0.082 3063 Dihedral : 14.784 111.049 6687 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.21 % Allowed : 10.93 % Favored : 88.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2115 helix: 2.35 (0.17), residues: 978 sheet: -2.47 (0.30), residues: 270 loop : -1.56 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.011 0.001 TYR A 692 PHE 0.012 0.001 PHE A1008 TRP 0.011 0.001 TRP A1213 HIS 0.010 0.001 HIS A1179 Details of bonding type rmsd covalent geometry : bond 0.00411 (17760) covalent geometry : angle 0.63795 (23998) hydrogen bonds : bond 0.17263 ( 908) hydrogen bonds : angle 6.57669 ( 2655) metal coordination : bond 0.44274 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 HIS cc_start: 0.6113 (t-90) cc_final: 0.5569 (t-90) REVERT: A 377 ILE cc_start: 0.4616 (mp) cc_final: 0.3746 (mt) REVERT: A 391 TYR cc_start: 0.7520 (m-80) cc_final: 0.7251 (m-80) REVERT: A 408 ARG cc_start: 0.6216 (mmt180) cc_final: 0.5915 (mmm160) REVERT: A 947 LEU cc_start: 0.4806 (tp) cc_final: 0.4343 (tt) REVERT: A 964 MET cc_start: 0.0232 (tmm) cc_final: -0.0135 (tpp) REVERT: C 102 MET cc_start: 0.5389 (mmt) cc_final: 0.4357 (mmt) REVERT: D 39 ILE cc_start: 0.6957 (mm) cc_final: 0.6437 (mp) REVERT: D 126 MET cc_start: 0.6238 (mmm) cc_final: 0.5999 (mtp) REVERT: D 159 CYS cc_start: 0.8555 (t) cc_final: 0.8138 (m) REVERT: D 162 TYR cc_start: 0.5504 (m-10) cc_final: 0.5282 (m-10) REVERT: D 172 MET cc_start: 0.5058 (mtm) cc_final: 0.4177 (mtp) REVERT: D 201 VAL cc_start: 0.8703 (t) cc_final: 0.8477 (p) REVERT: D 396 MET cc_start: 0.1529 (mtm) cc_final: -0.0345 (mmp) REVERT: E 513 MET cc_start: 0.0023 (tpt) cc_final: -0.0217 (mtp) outliers start: 4 outliers final: 2 residues processed: 367 average time/residue: 0.1583 time to fit residues: 83.6609 Evaluate side-chains 207 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain D residue 140 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 469 HIS A 525 ASN A 538 GLN A 592 HIS A 621 GLN A1173 GLN A1302 GLN B 62 GLN B 138 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS C 38 GLN C 88 ASN C 200 HIS C 460 HIS D 336 HIS D 420 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.205765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152988 restraints weight = 36646.792| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.72 r_work: 0.3808 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17763 Z= 0.237 Angle : 0.728 10.788 23998 Z= 0.376 Chirality : 0.045 0.180 2663 Planarity : 0.005 0.055 3063 Dihedral : 5.966 106.929 2340 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.59 % Allowed : 14.10 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2115 helix: 2.12 (0.16), residues: 964 sheet: -2.11 (0.29), residues: 297 loop : -1.27 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.023 0.002 TYR A1196 PHE 0.029 0.002 PHE A 663 TRP 0.019 0.002 TRP A1133 HIS 0.009 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00532 (17760) covalent geometry : angle 0.72780 (23998) hydrogen bonds : bond 0.06016 ( 908) hydrogen bonds : angle 4.82837 ( 2655) metal coordination : bond 0.01599 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 0.685 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 45 HIS cc_start: 0.6159 (t-90) cc_final: 0.5637 (t-90) REVERT: A 112 ASP cc_start: 0.7972 (m-30) cc_final: 0.7320 (p0) REVERT: A 150 LYS cc_start: 0.6449 (ttpp) cc_final: 0.5946 (ttpp) REVERT: A 408 ARG cc_start: 0.6874 (mmt180) cc_final: 0.6637 (mmm160) REVERT: A 753 ASN cc_start: 0.7738 (m-40) cc_final: 0.7353 (p0) REVERT: A 964 MET cc_start: 0.1067 (tmm) cc_final: -0.0126 (ttt) REVERT: A 965 MET cc_start: 0.2165 (mmt) cc_final: 0.1486 (tmm) REVERT: A 1025 MET cc_start: -0.0070 (tmm) cc_final: -0.0395 (tpp) REVERT: A 1133 TRP cc_start: 0.4658 (p90) cc_final: 0.3923 (p90) REVERT: A 1157 CYS cc_start: 0.4061 (OUTLIER) cc_final: 0.3738 (p) REVERT: A 1170 MET cc_start: 0.1408 (ppp) cc_final: -0.0546 (ptp) REVERT: B 76 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 78 TYR cc_start: 0.8267 (t80) cc_final: 0.7810 (t80) REVERT: B 96 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7061 (mttm) REVERT: B 142 ASP cc_start: 0.5464 (p0) cc_final: 0.5119 (p0) REVERT: B 254 LYS cc_start: 0.7832 (mtmm) cc_final: 0.6770 (tptt) REVERT: C 87 LYS cc_start: 0.8865 (pttt) cc_final: 0.8444 (pptt) REVERT: C 102 MET cc_start: 0.5863 (mmt) cc_final: 0.5070 (mmt) REVERT: C 295 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8735 (tt0) REVERT: D 126 MET cc_start: 0.6337 (mmm) cc_final: 0.5994 (mtp) REVERT: D 133 ASP cc_start: 0.7711 (p0) cc_final: 0.7308 (p0) REVERT: D 226 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6359 (mm-30) REVERT: D 261 LEU cc_start: 0.6430 (mp) cc_final: 0.5746 (pp) REVERT: D 396 MET cc_start: 0.2101 (mtm) cc_final: -0.0184 (mtt) outliers start: 69 outliers final: 32 residues processed: 260 average time/residue: 0.1461 time to fit residues: 56.4286 Evaluate side-chains 195 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1329 HIS Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 180 optimal weight: 9.9990 chunk 103 optimal weight: 0.0770 chunk 116 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 163 optimal weight: 0.0060 chunk 145 optimal weight: 0.7980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A1083 HIS B 141 HIS C 146 HIS D 315 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.207595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.154978 restraints weight = 37465.923| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 4.22 r_work: 0.3862 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17763 Z= 0.118 Angle : 0.544 9.069 23998 Z= 0.279 Chirality : 0.040 0.156 2663 Planarity : 0.004 0.040 3063 Dihedral : 5.217 99.271 2337 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.34 % Allowed : 15.24 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2115 helix: 2.55 (0.16), residues: 979 sheet: -1.82 (0.28), residues: 314 loop : -1.03 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 210 TYR 0.012 0.001 TYR D 233 PHE 0.015 0.001 PHE A 273 TRP 0.025 0.002 TRP A1168 HIS 0.006 0.001 HIS A1179 Details of bonding type rmsd covalent geometry : bond 0.00251 (17760) covalent geometry : angle 0.54385 (23998) hydrogen bonds : bond 0.04762 ( 908) hydrogen bonds : angle 4.25768 ( 2655) metal coordination : bond 0.00078 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.682 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 112 ASP cc_start: 0.7855 (m-30) cc_final: 0.7271 (p0) REVERT: A 293 MET cc_start: 0.5503 (mtp) cc_final: 0.5301 (mtp) REVERT: A 408 ARG cc_start: 0.6564 (mmt180) cc_final: 0.6342 (mmm160) REVERT: A 557 MET cc_start: 0.8488 (mpp) cc_final: 0.8009 (mmm) REVERT: A 581 MET cc_start: 0.7668 (mtp) cc_final: 0.7391 (mtm) REVERT: A 696 MET cc_start: 0.8176 (mmm) cc_final: 0.7843 (mmm) REVERT: A 753 ASN cc_start: 0.7661 (m-40) cc_final: 0.7371 (p0) REVERT: A 945 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6232 (tp-100) REVERT: A 964 MET cc_start: 0.1073 (tmm) cc_final: 0.0399 (ttt) REVERT: A 1170 MET cc_start: 0.2149 (ppp) cc_final: 0.1108 (ptp) REVERT: A 1266 ARG cc_start: 0.4389 (mpp80) cc_final: 0.3785 (mpp-170) REVERT: A 1275 ARG cc_start: 0.5182 (OUTLIER) cc_final: 0.4796 (tpt90) REVERT: B 11 TYR cc_start: 0.6465 (m-10) cc_final: 0.6214 (m-10) REVERT: B 78 TYR cc_start: 0.8325 (t80) cc_final: 0.7851 (t80) REVERT: B 96 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6938 (mttm) REVERT: B 142 ASP cc_start: 0.5285 (p0) cc_final: 0.4998 (p0) REVERT: B 254 LYS cc_start: 0.7754 (mtmm) cc_final: 0.6543 (tptt) REVERT: C 40 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6919 (ptp-170) REVERT: C 87 LYS cc_start: 0.8740 (pttt) cc_final: 0.8424 (pptt) REVERT: C 102 MET cc_start: 0.6160 (mmt) cc_final: 0.5383 (mmp) REVERT: C 295 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8720 (tt0) REVERT: D 126 MET cc_start: 0.6322 (mmm) cc_final: 0.6106 (mtp) REVERT: D 133 ASP cc_start: 0.7683 (p0) cc_final: 0.7127 (p0) REVERT: D 226 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6183 (mm-30) REVERT: D 396 MET cc_start: 0.0734 (mtm) cc_final: 0.0531 (mtt) REVERT: E 509 MET cc_start: -0.1815 (ppp) cc_final: -0.2806 (ttm) outliers start: 45 outliers final: 23 residues processed: 213 average time/residue: 0.1413 time to fit residues: 45.2190 Evaluate side-chains 181 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1329 HIS Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 277 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 147 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 580 HIS ** A1243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.200622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140506 restraints weight = 36297.809| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 5.38 r_work: 0.3703 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17763 Z= 0.217 Angle : 0.688 12.213 23998 Z= 0.352 Chirality : 0.045 0.192 2663 Planarity : 0.005 0.070 3063 Dihedral : 5.621 103.262 2337 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.90 % Allowed : 15.14 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2115 helix: 1.98 (0.16), residues: 980 sheet: -1.93 (0.28), residues: 308 loop : -1.23 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 30 TYR 0.018 0.002 TYR A 327 PHE 0.028 0.002 PHE D 372 TRP 0.031 0.003 TRP A1168 HIS 0.010 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00521 (17760) covalent geometry : angle 0.68850 (23998) hydrogen bonds : bond 0.05719 ( 908) hydrogen bonds : angle 4.61021 ( 2655) metal coordination : bond 0.00307 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.8539 (tp) cc_final: 0.8251 (tp) REVERT: A 286 ILE cc_start: 0.7501 (mp) cc_final: 0.7295 (mm) REVERT: A 333 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7217 (tppt) REVERT: A 408 ARG cc_start: 0.6680 (mmt180) cc_final: 0.6397 (mmm160) REVERT: A 477 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 945 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6237 (tp-100) REVERT: A 964 MET cc_start: 0.1275 (tmm) cc_final: 0.0473 (ttt) REVERT: A 1025 MET cc_start: 0.0058 (tmm) cc_final: -0.0582 (tpp) REVERT: A 1170 MET cc_start: 0.2402 (ppp) cc_final: 0.1473 (ptp) REVERT: B 78 TYR cc_start: 0.8657 (t80) cc_final: 0.8383 (t80) REVERT: B 96 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7550 (mttm) REVERT: B 133 TYR cc_start: 0.7859 (m-80) cc_final: 0.7519 (m-10) REVERT: B 258 PRO cc_start: 0.7169 (Cg_endo) cc_final: 0.6782 (Cg_exo) REVERT: C 40 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7579 (ptp-170) REVERT: C 102 MET cc_start: 0.6242 (mmt) cc_final: 0.5528 (mmp) REVERT: C 291 GLU cc_start: 0.8693 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 295 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8858 (mm-30) REVERT: C 320 GLN cc_start: 0.5279 (OUTLIER) cc_final: 0.4968 (pt0) REVERT: D 126 MET cc_start: 0.6480 (mmm) cc_final: 0.6224 (mtp) REVERT: D 133 ASP cc_start: 0.7764 (p0) cc_final: 0.7193 (p0) REVERT: D 152 LEU cc_start: 0.8798 (tt) cc_final: 0.8516 (tp) REVERT: D 172 MET cc_start: 0.4964 (mtp) cc_final: 0.4612 (mmm) REVERT: D 226 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6508 (mm-30) REVERT: D 247 LEU cc_start: 0.8764 (tt) cc_final: 0.8006 (tt) REVERT: D 321 MET cc_start: 0.4179 (mmt) cc_final: 0.3560 (ttp) REVERT: D 396 MET cc_start: 0.1364 (mtm) cc_final: 0.0291 (mmt) REVERT: D 415 ILE cc_start: 0.6352 (pt) cc_final: 0.6033 (pt) REVERT: E 514 MET cc_start: -0.4834 (tpp) cc_final: -0.5131 (tpt) outliers start: 75 outliers final: 47 residues processed: 232 average time/residue: 0.1282 time to fit residues: 44.8953 Evaluate side-chains 199 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1329 HIS Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 9 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 621 GLN ** A1243 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 = 0.4794 r_free = 0.4794 target = 0.201835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.144512 restraints weight = 36374.236| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 4.55 r_work: 0.3778 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17763 Z= 0.139 Angle : 0.582 10.361 23998 Z= 0.292 Chirality : 0.041 0.190 2663 Planarity : 0.004 0.050 3063 Dihedral : 5.174 95.436 2337 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.02 % Allowed : 17.01 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2115 helix: 2.32 (0.16), residues: 980 sheet: -1.64 (0.28), residues: 315 loop : -1.20 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 210 TYR 0.012 0.001 TYR B 58 PHE 0.039 0.002 PHE D 372 TRP 0.036 0.002 TRP C 94 HIS 0.006 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00323 (17760) covalent geometry : angle 0.58193 (23998) hydrogen bonds : bond 0.04650 ( 908) hydrogen bonds : angle 4.25339 ( 2655) metal coordination : bond 0.00109 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8279 (m-30) cc_final: 0.7964 (p0) REVERT: A 333 LYS cc_start: 0.7599 (ptpt) cc_final: 0.7319 (tppt) REVERT: A 408 ARG cc_start: 0.6280 (mmt180) cc_final: 0.5941 (mmm160) REVERT: A 415 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6680 (mp) REVERT: A 479 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7055 (mtt90) REVERT: A 696 MET cc_start: 0.8450 (mmm) cc_final: 0.8204 (mmm) REVERT: A 945 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6241 (tp40) REVERT: A 964 MET cc_start: 0.2055 (tmm) cc_final: 0.1354 (ttt) REVERT: A 1170 MET cc_start: 0.2696 (ppp) cc_final: 0.1843 (ptp) REVERT: B 76 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 96 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7664 (mttm) REVERT: B 133 TYR cc_start: 0.7639 (m-80) cc_final: 0.7305 (m-80) REVERT: C 40 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7522 (ptp-170) REVERT: C 102 MET cc_start: 0.6226 (mmt) cc_final: 0.5507 (mmp) REVERT: C 291 GLU cc_start: 0.8687 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 295 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8991 (mm-30) REVERT: C 299 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7729 (mp0) REVERT: C 320 GLN cc_start: 0.5593 (OUTLIER) cc_final: 0.5248 (pt0) REVERT: D 126 MET cc_start: 0.6306 (mmm) cc_final: 0.6099 (mtp) REVERT: D 133 ASP cc_start: 0.7733 (p0) cc_final: 0.7137 (p0) REVERT: D 172 MET cc_start: 0.4879 (mtp) cc_final: 0.4492 (mmm) REVERT: D 226 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6480 (mm-30) REVERT: D 251 GLU cc_start: 0.8184 (pt0) cc_final: 0.7960 (pp20) REVERT: D 396 MET cc_start: 0.0936 (mtm) cc_final: 0.0351 (mmt) REVERT: E 514 MET cc_start: -0.4782 (tpp) cc_final: -0.5010 (tpt) outliers start: 58 outliers final: 32 residues processed: 207 average time/residue: 0.1471 time to fit residues: 45.6213 Evaluate side-chains 185 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 90 optimal weight: 10.0000 chunk 111 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 167 optimal weight: 0.0970 chunk 45 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 131 GLN A 592 HIS A 753 ASN ** A1243 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 = 0.4829 r_free = 0.4829 target = 0.204925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.150821 restraints weight = 36851.264| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 5.07 r_work: 0.3835 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17763 Z= 0.104 Angle : 0.540 9.187 23998 Z= 0.269 Chirality : 0.039 0.189 2663 Planarity : 0.003 0.036 3063 Dihedral : 4.765 88.505 2337 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.24 % Allowed : 17.74 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 2115 helix: 2.69 (0.16), residues: 978 sheet: -1.31 (0.29), residues: 315 loop : -1.06 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 210 TYR 0.021 0.001 TYR B 78 PHE 0.025 0.001 PHE D 431 TRP 0.051 0.002 TRP A1020 HIS 0.004 0.001 HIS A1137 Details of bonding type rmsd covalent geometry : bond 0.00222 (17760) covalent geometry : angle 0.53985 (23998) hydrogen bonds : bond 0.04079 ( 908) hydrogen bonds : angle 4.00122 ( 2655) metal coordination : bond 0.00062 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.682 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: A 112 ASP cc_start: 0.8282 (m-30) cc_final: 0.7894 (p0) REVERT: A 286 ILE cc_start: 0.7616 (mm) cc_final: 0.7152 (mp) REVERT: A 333 LYS cc_start: 0.7592 (ptpt) cc_final: 0.7234 (tppt) REVERT: A 408 ARG cc_start: 0.6253 (mmt180) cc_final: 0.6000 (mmm160) REVERT: A 415 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6513 (mp) REVERT: A 964 MET cc_start: 0.2076 (tmm) cc_final: 0.1591 (ttt) REVERT: A 1025 MET cc_start: -0.0097 (tmm) cc_final: -0.0768 (tpp) REVERT: A 1170 MET cc_start: 0.2717 (ppp) cc_final: 0.1762 (ptt) REVERT: A 1275 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.4735 (tpt90) REVERT: B 96 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7590 (mttm) REVERT: B 133 TYR cc_start: 0.7502 (m-80) cc_final: 0.7273 (m-80) REVERT: B 138 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: B 172 MET cc_start: 0.3173 (tpt) cc_final: 0.2972 (tpt) REVERT: C 102 MET cc_start: 0.6127 (mmt) cc_final: 0.5461 (mmp) REVERT: C 291 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 295 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8852 (mm-30) REVERT: D 133 ASP cc_start: 0.7700 (p0) cc_final: 0.7113 (p0) REVERT: D 172 MET cc_start: 0.4937 (mtp) cc_final: 0.4562 (mmm) REVERT: D 226 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6619 (mm-30) REVERT: D 251 GLU cc_start: 0.8055 (pt0) cc_final: 0.7829 (pp20) REVERT: D 396 MET cc_start: 0.1098 (mtm) cc_final: -0.0022 (mmt) outliers start: 43 outliers final: 24 residues processed: 195 average time/residue: 0.1527 time to fit residues: 44.5549 Evaluate side-chains 172 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 394 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 27 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN A 554 GLN A 592 HIS A 709 GLN ** A1243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 367 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.197991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140736 restraints weight = 36487.824| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.71 r_work: 0.3685 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.8298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17763 Z= 0.221 Angle : 0.686 12.880 23998 Z= 0.346 Chirality : 0.045 0.253 2663 Planarity : 0.005 0.060 3063 Dihedral : 5.273 91.506 2337 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.64 % Allowed : 17.59 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 2115 helix: 1.97 (0.16), residues: 1001 sheet: -1.29 (0.30), residues: 288 loop : -1.28 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 210 TYR 0.035 0.002 TYR B 78 PHE 0.038 0.002 PHE A 130 TRP 0.060 0.003 TRP C 94 HIS 0.010 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00535 (17760) covalent geometry : angle 0.68577 (23998) hydrogen bonds : bond 0.05449 ( 908) hydrogen bonds : angle 4.47495 ( 2655) metal coordination : bond 0.00261 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 0.704 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: A 408 ARG cc_start: 0.6424 (mmt180) cc_final: 0.6076 (mmm160) REVERT: A 415 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6828 (mp) REVERT: A 479 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7332 (mtm110) REVERT: A 496 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 964 MET cc_start: 0.2555 (tmm) cc_final: 0.2245 (ttt) REVERT: A 1170 MET cc_start: 0.1941 (ppp) cc_final: 0.0943 (ptp) REVERT: A 1196 TYR cc_start: 0.7835 (m-80) cc_final: 0.7081 (m-80) REVERT: A 1275 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4738 (tpt90) REVERT: B 96 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7830 (mttm) REVERT: B 133 TYR cc_start: 0.7936 (m-80) cc_final: 0.7522 (m-10) REVERT: C 40 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7502 (ptp-170) REVERT: C 67 THR cc_start: 0.7911 (p) cc_final: 0.7637 (t) REVERT: C 102 MET cc_start: 0.6337 (mmt) cc_final: 0.5669 (mmp) REVERT: C 295 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8749 (mm-30) REVERT: D 133 ASP cc_start: 0.7724 (p0) cc_final: 0.7147 (p0) REVERT: D 172 MET cc_start: 0.4870 (mtp) cc_final: 0.4403 (mmm) REVERT: D 226 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6721 (mm-30) REVERT: D 321 MET cc_start: 0.3622 (mmt) cc_final: 0.2509 (ttt) outliers start: 70 outliers final: 42 residues processed: 209 average time/residue: 0.1352 time to fit residues: 43.4702 Evaluate side-chains 190 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 379 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 146 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 26 optimal weight: 0.0970 chunk 59 optimal weight: 0.1980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.201577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.147143 restraints weight = 36643.864| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 5.09 r_work: 0.3750 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17763 Z= 0.126 Angle : 0.596 11.657 23998 Z= 0.296 Chirality : 0.041 0.215 2663 Planarity : 0.004 0.043 3063 Dihedral : 4.887 86.918 2337 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.55 % Allowed : 19.20 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 2115 helix: 2.30 (0.16), residues: 1002 sheet: -1.13 (0.30), residues: 289 loop : -1.24 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 210 TYR 0.023 0.001 TYR B 78 PHE 0.025 0.001 PHE D 372 TRP 0.062 0.002 TRP C 94 HIS 0.005 0.001 HIS A1328 Details of bonding type rmsd covalent geometry : bond 0.00288 (17760) covalent geometry : angle 0.59622 (23998) hydrogen bonds : bond 0.04302 ( 908) hydrogen bonds : angle 4.16771 ( 2655) metal coordination : bond 0.00095 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7033 (mtm180) REVERT: A 112 ASP cc_start: 0.8377 (m-30) cc_final: 0.8002 (p0) REVERT: A 286 ILE cc_start: 0.7572 (mm) cc_final: 0.7030 (mp) REVERT: A 408 ARG cc_start: 0.6274 (mmt180) cc_final: 0.5939 (mmm160) REVERT: A 414 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7378 (mp) REVERT: A 415 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6603 (mp) REVERT: A 964 MET cc_start: 0.2730 (tmm) cc_final: 0.2386 (ttt) REVERT: A 1025 MET cc_start: 0.0040 (tmm) cc_final: -0.1032 (tpt) REVERT: A 1170 MET cc_start: 0.2094 (ppp) cc_final: 0.1160 (ptp) REVERT: A 1196 TYR cc_start: 0.7831 (m-80) cc_final: 0.6981 (m-80) REVERT: A 1275 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.4792 (tpt90) REVERT: B 96 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7906 (mttm) REVERT: B 133 TYR cc_start: 0.7832 (m-80) cc_final: 0.7492 (m-10) REVERT: C 94 TRP cc_start: 0.7868 (m-10) cc_final: 0.7279 (m-10) REVERT: C 102 MET cc_start: 0.6128 (mmt) cc_final: 0.5569 (mmp) REVERT: C 118 TRP cc_start: 0.7193 (m100) cc_final: 0.6901 (m100) REVERT: C 299 GLU cc_start: 0.7732 (pp20) cc_final: 0.7445 (pp20) REVERT: C 320 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5588 (pt0) REVERT: D 133 ASP cc_start: 0.7657 (p0) cc_final: 0.7283 (p0) REVERT: D 172 MET cc_start: 0.5138 (mtp) cc_final: 0.4582 (mmm) REVERT: D 214 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8680 (mmmm) REVERT: D 226 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6792 (mm-30) REVERT: D 252 ASN cc_start: 0.6547 (m-40) cc_final: 0.5919 (m110) REVERT: D 321 MET cc_start: 0.3833 (mmt) cc_final: 0.2748 (ttt) outliers start: 49 outliers final: 32 residues processed: 185 average time/residue: 0.1348 time to fit residues: 38.9086 Evaluate side-chains 174 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 214 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 70 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 76 optimal weight: 0.0030 chunk 65 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.197343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138987 restraints weight = 36616.595| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 4.87 r_work: 0.3680 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.9125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17763 Z= 0.203 Angle : 0.689 13.696 23998 Z= 0.344 Chirality : 0.044 0.250 2663 Planarity : 0.005 0.073 3063 Dihedral : 5.239 88.522 2337 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.02 % Allowed : 18.78 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2115 helix: 1.82 (0.16), residues: 1007 sheet: -1.16 (0.30), residues: 290 loop : -1.30 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 199 TYR 0.024 0.002 TYR B 78 PHE 0.038 0.002 PHE A 130 TRP 0.063 0.003 TRP C 94 HIS 0.007 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00485 (17760) covalent geometry : angle 0.68877 (23998) hydrogen bonds : bond 0.05191 ( 908) hydrogen bonds : angle 4.47128 ( 2655) metal coordination : bond 0.00252 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7081 (mtm180) REVERT: A 258 LEU cc_start: 0.8760 (tp) cc_final: 0.8509 (tp) REVERT: A 408 ARG cc_start: 0.6311 (mmt180) cc_final: 0.6057 (mmm160) REVERT: A 414 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 415 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 496 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 581 MET cc_start: 0.7646 (mtp) cc_final: 0.7365 (mtp) REVERT: A 964 MET cc_start: 0.2961 (tmm) cc_final: 0.2664 (ttt) REVERT: A 1025 MET cc_start: 0.0571 (tmm) cc_final: -0.0467 (tpp) REVERT: A 1170 MET cc_start: 0.2006 (ppp) cc_final: 0.1198 (ptp) REVERT: A 1196 TYR cc_start: 0.7905 (m-80) cc_final: 0.7143 (m-80) REVERT: A 1275 ARG cc_start: 0.5160 (OUTLIER) cc_final: 0.4942 (tpt90) REVERT: B 96 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7987 (mttm) REVERT: C 94 TRP cc_start: 0.8095 (m-10) cc_final: 0.7393 (m-10) REVERT: C 102 MET cc_start: 0.6219 (mmt) cc_final: 0.5812 (mmp) REVERT: C 118 TRP cc_start: 0.7391 (m100) cc_final: 0.6902 (m100) REVERT: C 306 LEU cc_start: 0.9253 (tp) cc_final: 0.8987 (mt) REVERT: C 320 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5720 (pt0) REVERT: D 133 ASP cc_start: 0.7856 (p0) cc_final: 0.7346 (p0) REVERT: D 172 MET cc_start: 0.5165 (mtp) cc_final: 0.4695 (mmm) REVERT: D 214 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8520 (mmmm) REVERT: D 226 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6874 (mm-30) REVERT: D 321 MET cc_start: 0.3908 (mmt) cc_final: 0.2831 (ttt) outliers start: 58 outliers final: 42 residues processed: 191 average time/residue: 0.1267 time to fit residues: 38.0222 Evaluate side-chains 188 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 127 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 0.0020 chunk 55 optimal weight: 0.0870 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.6208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.200487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.145906 restraints weight = 36553.027| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 5.03 r_work: 0.3747 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.9237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17763 Z= 0.125 Angle : 0.619 14.772 23998 Z= 0.302 Chirality : 0.042 0.312 2663 Planarity : 0.004 0.047 3063 Dihedral : 4.906 85.468 2337 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 19.88 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 2115 helix: 2.18 (0.16), residues: 1001 sheet: -0.90 (0.31), residues: 290 loop : -1.20 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 296 TYR 0.021 0.001 TYR B 78 PHE 0.028 0.001 PHE A1008 TRP 0.049 0.002 TRP C 94 HIS 0.007 0.001 HIS A 988 Details of bonding type rmsd covalent geometry : bond 0.00289 (17760) covalent geometry : angle 0.61893 (23998) hydrogen bonds : bond 0.04244 ( 908) hydrogen bonds : angle 4.21472 ( 2655) metal coordination : bond 0.00097 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7463 (mtt180) cc_final: 0.7119 (mtm180) REVERT: A 112 ASP cc_start: 0.8391 (m-30) cc_final: 0.8060 (p0) REVERT: A 408 ARG cc_start: 0.6252 (mmt180) cc_final: 0.5931 (mmm160) REVERT: A 414 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 415 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6593 (mp) REVERT: A 496 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 581 MET cc_start: 0.7587 (mtp) cc_final: 0.7298 (mtp) REVERT: A 964 MET cc_start: 0.2912 (tmm) cc_final: 0.2553 (ttt) REVERT: A 1025 MET cc_start: 0.0202 (tmm) cc_final: -0.0927 (tpp) REVERT: A 1170 MET cc_start: 0.2040 (ppp) cc_final: 0.1219 (ptp) REVERT: A 1196 TYR cc_start: 0.7930 (m-80) cc_final: 0.7030 (m-80) REVERT: A 1275 ARG cc_start: 0.5055 (OUTLIER) cc_final: 0.4821 (tpt90) REVERT: B 96 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7903 (mttm) REVERT: B 133 TYR cc_start: 0.8217 (m-80) cc_final: 0.8008 (m-10) REVERT: C 40 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7525 (ptp-170) REVERT: C 94 TRP cc_start: 0.7890 (m-10) cc_final: 0.7221 (m-10) REVERT: C 102 MET cc_start: 0.6103 (mmt) cc_final: 0.5640 (mmp) REVERT: C 118 TRP cc_start: 0.7249 (m100) cc_final: 0.6807 (m100) REVERT: C 306 LEU cc_start: 0.9252 (tp) cc_final: 0.8972 (mt) REVERT: C 320 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5704 (pt0) REVERT: C 458 MET cc_start: 0.1974 (ttt) cc_final: 0.1220 (ptp) REVERT: D 133 ASP cc_start: 0.7806 (p0) cc_final: 0.7292 (p0) REVERT: D 172 MET cc_start: 0.5187 (mtp) cc_final: 0.4643 (mmm) REVERT: D 214 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (mmmm) REVERT: D 226 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7009 (mm-30) REVERT: D 321 MET cc_start: 0.3762 (mmt) cc_final: 0.2702 (ttt) outliers start: 45 outliers final: 33 residues processed: 184 average time/residue: 0.1327 time to fit residues: 38.2718 Evaluate side-chains 180 residues out of total 1922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1338 PHE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.200049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.146942 restraints weight = 36512.828| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 5.16 r_work: 0.3732 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.9510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17763 Z= 0.141 Angle : 0.631 14.201 23998 Z= 0.309 Chirality : 0.042 0.233 2663 Planarity : 0.004 0.048 3063 Dihedral : 4.876 84.604 2337 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.45 % Allowed : 19.93 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2115 helix: 2.11 (0.16), residues: 1004 sheet: -0.82 (0.31), residues: 282 loop : -1.20 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 210 TYR 0.023 0.001 TYR B 78 PHE 0.026 0.001 PHE A1008 TRP 0.048 0.002 TRP C 94 HIS 0.005 0.001 HIS A1152 Details of bonding type rmsd covalent geometry : bond 0.00333 (17760) covalent geometry : angle 0.63072 (23998) hydrogen bonds : bond 0.04401 ( 908) hydrogen bonds : angle 4.26205 ( 2655) metal coordination : bond 0.00155 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.43 seconds wall clock time: 108 minutes 19.45 seconds (6499.45 seconds total)