Starting phenix.real_space_refine on Sun Feb 18 02:47:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmw_7967/02_2024/6dmw_7967_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.015 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 148 5.16 5 C 13254 2.51 5 N 3476 2.21 5 O 3665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20546 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5076 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 25, 'TRANS': 605} Chain breaks: 2 Chain: "E" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 2 Chain: "B" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4844 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.69, per 1000 atoms: 0.52 Number of scatterers: 20546 At special positions: 0 Unit cell: (134.2, 133.1, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 148 16.00 O 3665 8.00 N 3476 7.00 C 13254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 3.9 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4834 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 8 sheets defined 71.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.555A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.766A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.569A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.919A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.808A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.760A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 4.487A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.598A pdb=" N ASP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.564A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.984A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.614A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.856A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 removed outlier: 3.758A pdb=" N VAL A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.610A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.693A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.950A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.724A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.727A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 513 removed outlier: 4.188A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.729A pdb=" N LEU A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 4.108A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.714A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.163A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.711A pdb=" N LEU A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 4.086A pdb=" N VAL A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.549A pdb=" N ILE A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.545A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 39 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.793A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.537A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 119 through 130 removed outlier: 3.515A pdb=" N ASP E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.523A pdb=" N MET E 145 " --> pdb=" O GLU E 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.613A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.929A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.558A pdb=" N PHE B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.857A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.894A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.126A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 4.077A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.761A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.662A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.576A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 4.004A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.518A pdb=" N ASN B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 4.177A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.789A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 4.166A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.567A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.728A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.860A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 513 removed outlier: 4.286A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.730A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 4.019A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.914A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.019A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 600 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.745A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.835A pdb=" N GLU C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.898A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.516A pdb=" N PHE C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.603A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.771A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.704A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.657A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.673A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.745A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.522A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 379 through 410 removed outlier: 4.023A pdb=" N ILE C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.900A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.894A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 3.548A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.527A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 removed outlier: 3.805A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.920A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 489 " --> pdb=" O MET C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 4.148A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.852A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 4.415A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 586 Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.165A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.656A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.869A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.825A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.591A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 223 removed outlier: 4.147A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 4.133A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.024A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.933A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.797A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.635A pdb=" N ILE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.521A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.228A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 410' Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 445 removed outlier: 3.719A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.908A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 5.037A pdb=" N TYR D 467 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.871A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 513 removed outlier: 3.669A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.735A pdb=" N LEU D 520 " --> pdb=" O ASP D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.969A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 586 removed outlier: 4.993A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 4.259A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.519A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.807A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.776A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 618 " --> pdb=" O PHE B 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.858A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 635 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.938A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1110 hydrogen bonds defined for protein. 3216 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: 6.20 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6559 1.34 - 1.46: 4015 1.46 - 1.57: 10187 1.57 - 1.69: 0 1.69 - 1.81: 244 Bond restraints: 21005 Sorted by residual: bond pdb=" CB TRP A 583 " pdb=" CG TRP A 583 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.55e+00 bond pdb=" CG1 ILE C 501 " pdb=" CD1 ILE C 501 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CB TRP A 613 " pdb=" CG TRP A 613 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.27e+00 bond pdb=" CB PHE B 508 " pdb=" CG PHE B 508 " ideal model delta sigma weight residual 1.502 1.465 0.037 2.30e-02 1.89e+03 2.58e+00 bond pdb=" C GLY B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.331 1.319 0.012 7.90e-03 1.60e+04 2.42e+00 ... (remaining 21000 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.54: 362 104.54 - 111.96: 9958 111.96 - 119.39: 7430 119.39 - 126.81: 10456 126.81 - 134.24: 288 Bond angle restraints: 28494 Sorted by residual: angle pdb=" N ILE D 510 " pdb=" CA ILE D 510 " pdb=" C ILE D 510 " ideal model delta sigma weight residual 111.91 106.96 4.95 8.90e-01 1.26e+00 3.10e+01 angle pdb=" C ASN B 127 " pdb=" N GLN B 128 " pdb=" CA GLN B 128 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.33e+01 angle pdb=" N THR C 311 " pdb=" CA THR C 311 " pdb=" C THR C 311 " ideal model delta sigma weight residual 112.75 117.60 -4.85 1.36e+00 5.41e-01 1.27e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 112.34 119.40 -7.06 2.04e+00 2.40e-01 1.20e+01 angle pdb=" C GLY B 521 " pdb=" N GLU B 522 " pdb=" CA GLU B 522 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 ... (remaining 28489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11549 15.07 - 30.13: 708 30.13 - 45.20: 222 45.20 - 60.26: 15 60.26 - 75.33: 15 Dihedral angle restraints: 12509 sinusoidal: 5034 harmonic: 7475 Sorted by residual: dihedral pdb=" CA ASP B 193 " pdb=" C ASP B 193 " pdb=" N SER B 194 " pdb=" CA SER B 194 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N HIS A 165 " pdb=" CA HIS A 165 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA GLU D 164 " pdb=" C GLU D 164 " pdb=" N HIS D 165 " pdb=" CA HIS D 165 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 12506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2354 0.056 - 0.112: 704 0.112 - 0.167: 153 0.167 - 0.223: 21 0.223 - 0.279: 4 Chirality restraints: 3236 Sorted by residual: chirality pdb=" CG LEU C 352 " pdb=" CB LEU C 352 " pdb=" CD1 LEU C 352 " pdb=" CD2 LEU C 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE D 510 " pdb=" CA ILE D 510 " pdb=" CG1 ILE D 510 " pdb=" CG2 ILE D 510 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3233 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 311 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 312 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 585 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C VAL D 585 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 585 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 586 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 623 " -0.024 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR D 623 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 623 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 623 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 623 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 623 " -0.001 2.00e-02 2.50e+03 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5158 2.78 - 3.31: 20475 3.31 - 3.84: 34703 3.84 - 4.37: 38378 4.37 - 4.90: 61439 Nonbonded interactions: 160153 Sorted by model distance: nonbonded pdb=" N VAL B 378 " pdb=" OD2 ASP B 382 " model vdw 2.253 2.520 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.268 2.440 nonbonded pdb=" O HIS D 165 " pdb=" OG SER D 168 " model vdw 2.278 2.440 nonbonded pdb=" NH2 ARG A 359 " pdb=" O THR A 366 " model vdw 2.284 2.520 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.285 2.440 ... (remaining 160148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 225 or resid 231 through 638)) selection = chain 'B' selection = (chain 'C' and (resid 29 through 225 or resid 231 through 638)) selection = (chain 'D' and (resid 29 through 225 or resid 231 through 638)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.840 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 53.400 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.006 0.071 21005 Z= 0.413 Angle : 1.017 10.179 28494 Z= 0.548 Chirality : 0.055 0.279 3236 Planarity : 0.007 0.069 3618 Dihedral : 11.364 75.325 7675 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.13), residues: 2538 helix: -2.13 (0.10), residues: 1544 sheet: -3.32 (0.56), residues: 58 loop : -2.08 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 613 HIS 0.013 0.003 HIS B 426 PHE 0.037 0.003 PHE A 508 TYR 0.040 0.003 TYR D 623 ARG 0.016 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 680 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 VAL cc_start: 0.9390 (t) cc_final: 0.9106 (p) REVERT: A 197 ASN cc_start: 0.8779 (m110) cc_final: 0.8469 (t0) REVERT: A 255 MET cc_start: 0.8276 (tpp) cc_final: 0.7782 (tpp) REVERT: A 294 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8283 (pt0) REVERT: A 340 MET cc_start: 0.7812 (tpp) cc_final: 0.7570 (tpp) REVERT: A 445 THR cc_start: 0.5967 (p) cc_final: 0.5730 (p) REVERT: A 447 MET cc_start: 0.4455 (tpt) cc_final: 0.4198 (tpt) REVERT: A 464 SER cc_start: 0.9286 (t) cc_final: 0.8850 (p) REVERT: A 520 LEU cc_start: 0.4410 (pp) cc_final: 0.3617 (pp) REVERT: A 535 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6424 (mt-10) REVERT: A 546 ASN cc_start: 0.7615 (m-40) cc_final: 0.7214 (t0) REVERT: A 553 PHE cc_start: 0.8384 (t80) cc_final: 0.7920 (t80) REVERT: A 577 MET cc_start: 0.8671 (tmm) cc_final: 0.8383 (tmm) REVERT: A 591 GLU cc_start: 0.8281 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 643 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6911 (ptt180) REVERT: E 37 MET cc_start: 0.6491 (mmm) cc_final: 0.5728 (tpt) REVERT: E 76 LYS cc_start: 0.7997 (tppt) cc_final: 0.7793 (tptp) REVERT: E 101 ILE cc_start: 0.5195 (mt) cc_final: 0.4908 (mt) REVERT: E 110 MET cc_start: 0.5985 (tpp) cc_final: 0.5728 (mmt) REVERT: E 125 MET cc_start: 0.7391 (mtp) cc_final: 0.7097 (mmp) REVERT: E 138 ASN cc_start: 0.6462 (p0) cc_final: 0.5890 (p0) REVERT: E 139 TYR cc_start: 0.7530 (t80) cc_final: 0.7267 (t80) REVERT: E 146 MET cc_start: 0.2885 (mmm) cc_final: 0.1894 (mmt) REVERT: B 91 ASN cc_start: 0.6891 (m-40) cc_final: 0.6219 (m110) REVERT: B 162 TYR cc_start: 0.8006 (m-10) cc_final: 0.7805 (m-10) REVERT: B 183 ILE cc_start: 0.7953 (mt) cc_final: 0.7466 (mm) REVERT: B 208 ASN cc_start: 0.8125 (p0) cc_final: 0.7242 (p0) REVERT: B 294 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8840 (pt0) REVERT: B 306 GLN cc_start: 0.7932 (tt0) cc_final: 0.7626 (tp40) REVERT: B 389 GLU cc_start: 0.7558 (tt0) cc_final: 0.7084 (tm-30) REVERT: B 444 LEU cc_start: 0.9018 (mt) cc_final: 0.8711 (mm) REVERT: B 546 ASN cc_start: 0.8349 (m-40) cc_final: 0.7688 (t0) REVERT: B 580 ASP cc_start: 0.5012 (t0) cc_final: 0.3920 (t0) REVERT: B 638 ASP cc_start: 0.6674 (m-30) cc_final: 0.6468 (m-30) REVERT: C 368 LEU cc_start: 0.7994 (tp) cc_final: 0.7585 (tp) REVERT: C 389 GLU cc_start: 0.8503 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 580 ASP cc_start: 0.5755 (t0) cc_final: 0.4875 (t70) REVERT: C 583 TRP cc_start: 0.7621 (t60) cc_final: 0.6994 (t60) REVERT: C 603 MET cc_start: 0.8066 (tmt) cc_final: 0.7852 (tmm) REVERT: D 65 LEU cc_start: 0.9372 (mm) cc_final: 0.9061 (mm) REVERT: D 467 TYR cc_start: 0.6830 (t80) cc_final: 0.6582 (t80) REVERT: D 474 MET cc_start: 0.7380 (ptt) cc_final: 0.7106 (ptm) REVERT: D 499 VAL cc_start: 0.7092 (t) cc_final: 0.6830 (p) REVERT: D 520 LEU cc_start: 0.3932 (pp) cc_final: 0.3410 (pp) outliers start: 4 outliers final: 0 residues processed: 681 average time/residue: 0.3271 time to fit residues: 334.0269 Evaluate side-chains 358 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 106 optimal weight: 0.0670 chunk 65 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 230 GLN A 257 GLN A 708 ASN B 37 ASN B 513 GLN B 636 HIS C 84 HIS C 267 GLN C 513 GLN D 192 GLN D 206 GLN D 230 GLN D 582 HIS D 636 HIS D 637 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21005 Z= 0.227 Angle : 0.660 9.884 28494 Z= 0.338 Chirality : 0.039 0.152 3236 Planarity : 0.005 0.050 3618 Dihedral : 5.247 24.636 2792 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2538 helix: -0.27 (0.12), residues: 1593 sheet: -2.79 (0.58), residues: 61 loop : -1.95 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 613 HIS 0.006 0.001 HIS D 258 PHE 0.025 0.002 PHE A 456 TYR 0.015 0.002 TYR B 89 ARG 0.035 0.001 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 461 time to evaluate : 2.448 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 255 MET cc_start: 0.7931 (tpp) cc_final: 0.7716 (tpp) REVERT: A 442 MET cc_start: 0.7813 (tpp) cc_final: 0.7401 (tmm) REVERT: A 520 LEU cc_start: 0.4187 (pp) cc_final: 0.3329 (pp) REVERT: A 535 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 553 PHE cc_start: 0.8283 (t80) cc_final: 0.7985 (t80) REVERT: A 577 MET cc_start: 0.8592 (tmm) cc_final: 0.8328 (tmm) REVERT: A 591 GLU cc_start: 0.8416 (tt0) cc_final: 0.8109 (tm-30) REVERT: E 37 MET cc_start: 0.6540 (mmm) cc_final: 0.5992 (tpt) REVERT: E 101 ILE cc_start: 0.5309 (mt) cc_final: 0.5045 (mt) REVERT: E 110 MET cc_start: 0.6009 (tpp) cc_final: 0.5476 (tpp) REVERT: E 125 MET cc_start: 0.7305 (mtp) cc_final: 0.6991 (mmt) REVERT: E 128 GLU cc_start: 0.5686 (tt0) cc_final: 0.5351 (tt0) REVERT: B 211 PHE cc_start: 0.8701 (p90) cc_final: 0.8434 (p90) REVERT: B 260 MET cc_start: 0.8210 (tpp) cc_final: 0.7986 (tpp) REVERT: B 294 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8792 (pt0) REVERT: B 306 GLN cc_start: 0.8243 (tt0) cc_final: 0.7959 (tp40) REVERT: B 403 GLU cc_start: 0.8706 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 546 ASN cc_start: 0.8033 (m-40) cc_final: 0.7543 (t0) REVERT: B 580 ASP cc_start: 0.5889 (t0) cc_final: 0.4780 (t0) REVERT: C 392 THR cc_start: 0.8219 (m) cc_final: 0.7840 (m) REVERT: C 447 MET cc_start: 0.5404 (mmm) cc_final: 0.5181 (mmm) REVERT: C 485 MET cc_start: 0.7131 (tpp) cc_final: 0.6765 (tpp) REVERT: D 173 VAL cc_start: 0.7170 (p) cc_final: 0.6824 (p) REVERT: D 474 MET cc_start: 0.7362 (ptt) cc_final: 0.7044 (ptm) REVERT: D 483 GLN cc_start: 0.8237 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 520 LEU cc_start: 0.3550 (pp) cc_final: 0.2949 (pp) outliers start: 2 outliers final: 0 residues processed: 463 average time/residue: 0.3016 time to fit residues: 217.7798 Evaluate side-chains 291 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 205 optimal weight: 40.0000 chunk 229 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 37 ASN B 158 ASN B 197 ASN B 265 HIS B 513 GLN C 206 GLN C 513 GLN D 230 GLN D 582 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21005 Z= 0.293 Angle : 0.687 7.900 28494 Z= 0.353 Chirality : 0.041 0.232 3236 Planarity : 0.005 0.060 3618 Dihedral : 4.925 23.461 2792 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2538 helix: 0.44 (0.13), residues: 1582 sheet: -2.42 (0.55), residues: 63 loop : -1.70 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 613 HIS 0.008 0.001 HIS D 258 PHE 0.024 0.002 PHE A 512 TYR 0.024 0.002 TYR D 162 ARG 0.008 0.001 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 357 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 215 MET cc_start: 0.8935 (tmm) cc_final: 0.8547 (tmm) REVERT: A 255 MET cc_start: 0.7907 (tpp) cc_final: 0.7683 (tpp) REVERT: A 368 LEU cc_start: 0.8361 (mm) cc_final: 0.7996 (mm) REVERT: A 520 LEU cc_start: 0.4003 (pp) cc_final: 0.3495 (pp) REVERT: A 535 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6387 (mt-10) REVERT: A 577 MET cc_start: 0.8633 (tmm) cc_final: 0.8405 (tmm) REVERT: A 591 GLU cc_start: 0.8363 (tt0) cc_final: 0.8062 (tm-30) REVERT: A 643 ARG cc_start: 0.7590 (ptt180) cc_final: 0.7219 (ptt180) REVERT: E 37 MET cc_start: 0.6392 (mmm) cc_final: 0.5826 (tpt) REVERT: E 86 ILE cc_start: 0.6420 (mm) cc_final: 0.5905 (mm) REVERT: E 125 MET cc_start: 0.7463 (mtp) cc_final: 0.7074 (mmt) REVERT: E 128 GLU cc_start: 0.6257 (tt0) cc_final: 0.5944 (tt0) REVERT: B 93 GLU cc_start: 0.8914 (mp0) cc_final: 0.8686 (pm20) REVERT: B 260 MET cc_start: 0.8165 (tpp) cc_final: 0.7888 (tpp) REVERT: B 294 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8752 (pt0) REVERT: B 515 GLU cc_start: 0.8704 (tp30) cc_final: 0.7914 (mm-30) REVERT: B 546 ASN cc_start: 0.8014 (m-40) cc_final: 0.7615 (t0) REVERT: B 612 LEU cc_start: 0.8285 (mt) cc_final: 0.8031 (mt) REVERT: C 255 MET cc_start: 0.8182 (tpp) cc_final: 0.7974 (tpp) REVERT: C 447 MET cc_start: 0.5640 (mmm) cc_final: 0.5368 (mmm) REVERT: C 485 MET cc_start: 0.6669 (tpp) cc_final: 0.6341 (tpt) REVERT: C 537 PHE cc_start: 0.8337 (t80) cc_final: 0.8108 (t80) REVERT: D 162 TYR cc_start: 0.8243 (m-80) cc_final: 0.7783 (m-10) REVERT: D 283 ILE cc_start: 0.8103 (tp) cc_final: 0.7889 (mp) REVERT: D 474 MET cc_start: 0.7649 (ptt) cc_final: 0.7387 (ptm) REVERT: D 485 MET cc_start: 0.7641 (tpp) cc_final: 0.7427 (tpp) REVERT: D 520 LEU cc_start: 0.3913 (pp) cc_final: 0.3550 (pp) outliers start: 3 outliers final: 1 residues processed: 358 average time/residue: 0.2865 time to fit residues: 164.2746 Evaluate side-chains 254 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 0.2980 chunk 173 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 219 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 37 ASN B 513 GLN B 546 ASN B 636 HIS C 418 GLN C 513 GLN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 21005 Z= 0.166 Angle : 0.596 7.944 28494 Z= 0.296 Chirality : 0.038 0.152 3236 Planarity : 0.004 0.033 3618 Dihedral : 4.629 22.907 2792 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2538 helix: 0.89 (0.13), residues: 1582 sheet: -1.93 (0.55), residues: 65 loop : -1.61 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 583 HIS 0.006 0.001 HIS D 258 PHE 0.024 0.001 PHE E 20 TYR 0.035 0.001 TYR C 162 ARG 0.006 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9187 (mtm) cc_final: 0.8967 (mtp) REVERT: A 162 TYR cc_start: 0.8729 (m-10) cc_final: 0.8418 (m-10) REVERT: A 176 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 215 MET cc_start: 0.8935 (tmm) cc_final: 0.8677 (tmm) REVERT: A 294 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8217 (pt0) REVERT: A 368 LEU cc_start: 0.8396 (mm) cc_final: 0.8028 (mm) REVERT: A 442 MET cc_start: 0.7971 (tpp) cc_final: 0.7536 (tmm) REVERT: A 520 LEU cc_start: 0.4097 (pp) cc_final: 0.3793 (pp) REVERT: A 535 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6332 (mt-10) REVERT: A 591 GLU cc_start: 0.8245 (tt0) cc_final: 0.7940 (tm-30) REVERT: A 627 ASP cc_start: 0.8888 (m-30) cc_final: 0.8220 (t0) REVERT: A 643 ARG cc_start: 0.7528 (ptt180) cc_final: 0.7021 (ptt180) REVERT: E 28 ILE cc_start: 0.5754 (tp) cc_final: 0.5419 (tp) REVERT: E 37 MET cc_start: 0.6170 (mmm) cc_final: 0.5577 (tpt) REVERT: E 86 ILE cc_start: 0.6537 (mm) cc_final: 0.5918 (mm) REVERT: E 115 GLU cc_start: 0.6263 (pm20) cc_final: 0.6059 (pm20) REVERT: E 125 MET cc_start: 0.7202 (mtp) cc_final: 0.6771 (mmt) REVERT: E 128 GLU cc_start: 0.6447 (tt0) cc_final: 0.6151 (tt0) REVERT: B 55 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 91 ASN cc_start: 0.6531 (m-40) cc_final: 0.5940 (m-40) REVERT: B 211 PHE cc_start: 0.8467 (p90) cc_final: 0.8120 (p90) REVERT: B 260 MET cc_start: 0.8178 (tpp) cc_final: 0.7971 (tpp) REVERT: B 294 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8743 (pt0) REVERT: B 306 GLN cc_start: 0.8212 (tp40) cc_final: 0.7994 (tp40) REVERT: B 515 GLU cc_start: 0.8603 (tp30) cc_final: 0.7925 (mm-30) REVERT: B 535 GLU cc_start: 0.7020 (mp0) cc_final: 0.6777 (mp0) REVERT: B 546 ASN cc_start: 0.7889 (m110) cc_final: 0.7467 (t0) REVERT: B 612 LEU cc_start: 0.8310 (mt) cc_final: 0.8073 (mt) REVERT: C 447 MET cc_start: 0.5659 (mmm) cc_final: 0.5382 (mmm) REVERT: D 65 LEU cc_start: 0.9393 (mm) cc_final: 0.9168 (pp) REVERT: D 91 ASN cc_start: 0.6799 (m-40) cc_final: 0.6237 (m110) REVERT: D 125 VAL cc_start: 0.8782 (m) cc_final: 0.8515 (p) REVERT: D 162 TYR cc_start: 0.7992 (m-80) cc_final: 0.7586 (m-80) REVERT: D 474 MET cc_start: 0.7599 (ptt) cc_final: 0.7352 (ptm) REVERT: D 520 LEU cc_start: 0.3947 (pp) cc_final: 0.3547 (pp) outliers start: 1 outliers final: 1 residues processed: 375 average time/residue: 0.2745 time to fit residues: 166.3625 Evaluate side-chains 283 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 37 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 546 ASN C 225 HIS C 418 GLN C 513 GLN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21005 Z= 0.260 Angle : 0.639 8.036 28494 Z= 0.326 Chirality : 0.040 0.161 3236 Planarity : 0.004 0.032 3618 Dihedral : 4.557 20.826 2792 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2538 helix: 1.04 (0.13), residues: 1579 sheet: -2.17 (0.51), residues: 73 loop : -1.58 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 613 HIS 0.006 0.001 HIS D 258 PHE 0.021 0.002 PHE D 512 TYR 0.021 0.002 TYR A 526 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9216 (mtm) cc_final: 0.8958 (mtp) REVERT: A 112 CYS cc_start: 0.6080 (t) cc_final: 0.5880 (t) REVERT: A 176 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8382 (mm-30) REVERT: A 215 MET cc_start: 0.8998 (tmm) cc_final: 0.8588 (tmm) REVERT: A 294 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8155 (pt0) REVERT: A 368 LEU cc_start: 0.8376 (mm) cc_final: 0.8003 (mm) REVERT: A 442 MET cc_start: 0.8131 (tpp) cc_final: 0.7813 (tpp) REVERT: A 520 LEU cc_start: 0.3976 (pp) cc_final: 0.3488 (pp) REVERT: A 535 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6207 (mt-10) REVERT: A 627 ASP cc_start: 0.9030 (m-30) cc_final: 0.8343 (t0) REVERT: A 643 ARG cc_start: 0.7564 (ptt180) cc_final: 0.7121 (ptt180) REVERT: E 28 ILE cc_start: 0.5746 (tp) cc_final: 0.5314 (tp) REVERT: E 37 MET cc_start: 0.6224 (mmm) cc_final: 0.5657 (tpt) REVERT: E 86 ILE cc_start: 0.6595 (mm) cc_final: 0.5988 (mm) REVERT: E 90 PHE cc_start: 0.7226 (t80) cc_final: 0.6935 (t80) REVERT: E 110 MET cc_start: 0.6104 (tpp) cc_final: 0.5857 (mmt) REVERT: E 125 MET cc_start: 0.7221 (mtp) cc_final: 0.6819 (mmt) REVERT: E 128 GLU cc_start: 0.6614 (tt0) cc_final: 0.6191 (tt0) REVERT: B 55 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 91 ASN cc_start: 0.6534 (m-40) cc_final: 0.6006 (m-40) REVERT: B 159 LEU cc_start: 0.9014 (mm) cc_final: 0.8757 (mt) REVERT: B 211 PHE cc_start: 0.8409 (p90) cc_final: 0.8037 (p90) REVERT: B 260 MET cc_start: 0.8250 (tpp) cc_final: 0.8005 (tpp) REVERT: B 294 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8661 (pt0) REVERT: B 515 GLU cc_start: 0.8765 (tp30) cc_final: 0.8172 (mm-30) REVERT: B 535 GLU cc_start: 0.6796 (mp0) cc_final: 0.6467 (mp0) REVERT: B 546 ASN cc_start: 0.7953 (m-40) cc_final: 0.7473 (t0) REVERT: B 612 LEU cc_start: 0.8283 (mt) cc_final: 0.8028 (mt) REVERT: C 112 CYS cc_start: 0.2528 (t) cc_final: 0.1820 (t) REVERT: C 447 MET cc_start: 0.5743 (mmm) cc_final: 0.5471 (mmm) REVERT: C 570 MET cc_start: 0.5928 (pmm) cc_final: 0.5726 (pmm) REVERT: D 91 ASN cc_start: 0.6794 (m-40) cc_final: 0.6224 (m110) REVERT: D 125 VAL cc_start: 0.8795 (m) cc_final: 0.8550 (p) REVERT: D 162 TYR cc_start: 0.8099 (m-80) cc_final: 0.7792 (m-10) REVERT: D 474 MET cc_start: 0.7651 (ptt) cc_final: 0.7315 (ttp) REVERT: D 520 LEU cc_start: 0.3883 (pp) cc_final: 0.3425 (pp) outliers start: 1 outliers final: 1 residues processed: 343 average time/residue: 0.2794 time to fit residues: 156.3617 Evaluate side-chains 258 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 245 optimal weight: 0.0870 chunk 204 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 546 ASN C 128 GLN C 418 GLN C 513 GLN D 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21005 Z= 0.174 Angle : 0.598 8.095 28494 Z= 0.297 Chirality : 0.038 0.155 3236 Planarity : 0.003 0.032 3618 Dihedral : 4.428 19.504 2792 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2538 helix: 1.21 (0.13), residues: 1580 sheet: -2.09 (0.50), residues: 73 loop : -1.52 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 702 HIS 0.006 0.001 HIS D 258 PHE 0.028 0.001 PHE B 531 TYR 0.040 0.001 TYR C 162 ARG 0.005 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9197 (mtm) cc_final: 0.8924 (mtp) REVERT: A 176 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 215 MET cc_start: 0.8982 (tmm) cc_final: 0.8749 (tmm) REVERT: A 294 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8121 (pt0) REVERT: A 368 LEU cc_start: 0.8268 (mm) cc_final: 0.7998 (mm) REVERT: A 442 MET cc_start: 0.8188 (tpp) cc_final: 0.7916 (tpp) REVERT: A 520 LEU cc_start: 0.3969 (pp) cc_final: 0.3518 (pp) REVERT: A 535 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6305 (mt-10) REVERT: A 627 ASP cc_start: 0.9076 (m-30) cc_final: 0.8384 (t0) REVERT: A 643 ARG cc_start: 0.7623 (ptt180) cc_final: 0.7280 (ptt180) REVERT: E 28 ILE cc_start: 0.5815 (tp) cc_final: 0.5524 (tp) REVERT: E 37 MET cc_start: 0.6232 (mmm) cc_final: 0.5680 (tpt) REVERT: E 86 ILE cc_start: 0.6722 (mm) cc_final: 0.6155 (mm) REVERT: E 90 PHE cc_start: 0.7212 (t80) cc_final: 0.6950 (t80) REVERT: E 125 MET cc_start: 0.7342 (mtp) cc_final: 0.6871 (mmp) REVERT: E 128 GLU cc_start: 0.6787 (tt0) cc_final: 0.6568 (tt0) REVERT: B 91 ASN cc_start: 0.6390 (m-40) cc_final: 0.5878 (m-40) REVERT: B 159 LEU cc_start: 0.9026 (mm) cc_final: 0.8767 (mt) REVERT: B 211 PHE cc_start: 0.8410 (p90) cc_final: 0.8097 (p90) REVERT: B 294 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8643 (pt0) REVERT: B 447 MET cc_start: 0.5573 (tpt) cc_final: 0.4799 (ttt) REVERT: B 515 GLU cc_start: 0.8719 (tp30) cc_final: 0.8069 (mm-30) REVERT: B 546 ASN cc_start: 0.7903 (m110) cc_final: 0.7480 (t0) REVERT: B 612 LEU cc_start: 0.8267 (mt) cc_final: 0.7996 (mt) REVERT: C 112 CYS cc_start: 0.2304 (t) cc_final: 0.1516 (t) REVERT: C 215 MET cc_start: 0.8628 (tmm) cc_final: 0.8405 (tmm) REVERT: C 447 MET cc_start: 0.5769 (mmm) cc_final: 0.5508 (mmm) REVERT: D 91 ASN cc_start: 0.6861 (m-40) cc_final: 0.6335 (m110) REVERT: D 125 VAL cc_start: 0.8765 (m) cc_final: 0.8512 (p) REVERT: D 162 TYR cc_start: 0.7962 (m-10) cc_final: 0.7578 (m-80) REVERT: D 474 MET cc_start: 0.7654 (ptt) cc_final: 0.7354 (ttp) REVERT: D 520 LEU cc_start: 0.3982 (pp) cc_final: 0.3588 (pp) outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.2793 time to fit residues: 153.5124 Evaluate side-chains 272 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 0.0070 chunk 140 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 244 optimal weight: 0.4980 chunk 153 optimal weight: 0.2980 chunk 149 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 37 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 636 HIS C 418 GLN C 513 GLN D 230 GLN D 596 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21005 Z= 0.154 Angle : 0.587 8.779 28494 Z= 0.289 Chirality : 0.038 0.152 3236 Planarity : 0.003 0.032 3618 Dihedral : 4.282 19.369 2792 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2538 helix: 1.34 (0.13), residues: 1577 sheet: -1.94 (0.49), residues: 73 loop : -1.44 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 702 HIS 0.005 0.001 HIS D 258 PHE 0.036 0.001 PHE B 531 TYR 0.020 0.001 TYR C 162 ARG 0.006 0.000 ARG D 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9192 (mtm) cc_final: 0.8924 (mtp) REVERT: A 176 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 294 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8093 (pt0) REVERT: A 368 LEU cc_start: 0.8263 (mm) cc_final: 0.8006 (mm) REVERT: A 442 MET cc_start: 0.8282 (tpp) cc_final: 0.8001 (tpp) REVERT: A 520 LEU cc_start: 0.3824 (pp) cc_final: 0.3068 (pp) REVERT: A 535 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6320 (mt-10) REVERT: A 627 ASP cc_start: 0.9115 (m-30) cc_final: 0.8388 (t0) REVERT: A 643 ARG cc_start: 0.7598 (ptt180) cc_final: 0.7189 (ptt180) REVERT: E 28 ILE cc_start: 0.5675 (tp) cc_final: 0.5353 (tp) REVERT: E 37 MET cc_start: 0.6208 (mmm) cc_final: 0.5666 (tpt) REVERT: E 86 ILE cc_start: 0.6633 (mm) cc_final: 0.6112 (mm) REVERT: E 90 PHE cc_start: 0.7223 (t80) cc_final: 0.6971 (t80) REVERT: E 125 MET cc_start: 0.7374 (mtp) cc_final: 0.6891 (mmt) REVERT: E 128 GLU cc_start: 0.6875 (tt0) cc_final: 0.6592 (tt0) REVERT: B 55 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 91 ASN cc_start: 0.6521 (m-40) cc_final: 0.5973 (m-40) REVERT: B 159 LEU cc_start: 0.9054 (mm) cc_final: 0.8798 (mt) REVERT: B 211 PHE cc_start: 0.8415 (p90) cc_final: 0.8035 (p90) REVERT: B 294 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8636 (pt0) REVERT: B 474 MET cc_start: 0.8013 (ptp) cc_final: 0.7768 (ptp) REVERT: B 515 GLU cc_start: 0.8616 (tp30) cc_final: 0.8046 (mm-30) REVERT: B 546 ASN cc_start: 0.7957 (m110) cc_final: 0.7444 (t0) REVERT: B 612 LEU cc_start: 0.8229 (mt) cc_final: 0.7983 (mt) REVERT: C 112 CYS cc_start: 0.2459 (t) cc_final: 0.1707 (t) REVERT: C 447 MET cc_start: 0.5795 (mmm) cc_final: 0.5527 (mmm) REVERT: D 91 ASN cc_start: 0.6922 (m-40) cc_final: 0.6402 (m110) REVERT: D 162 TYR cc_start: 0.7938 (m-10) cc_final: 0.7503 (m-80) REVERT: D 425 PHE cc_start: 0.6366 (m-80) cc_final: 0.6153 (m-80) REVERT: D 474 MET cc_start: 0.7663 (ptt) cc_final: 0.7399 (ptm) REVERT: D 520 LEU cc_start: 0.3887 (pp) cc_final: 0.3558 (pp) outliers start: 1 outliers final: 1 residues processed: 357 average time/residue: 0.2727 time to fit residues: 159.1507 Evaluate side-chains 267 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN C 418 GLN C 513 GLN D 37 ASN D 230 GLN D 596 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21005 Z= 0.182 Angle : 0.601 8.680 28494 Z= 0.299 Chirality : 0.039 0.153 3236 Planarity : 0.003 0.032 3618 Dihedral : 4.251 18.317 2792 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.05 % Allowed : 0.99 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2538 helix: 1.31 (0.13), residues: 1587 sheet: -1.55 (0.51), residues: 68 loop : -1.40 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 702 HIS 0.006 0.001 HIS B 258 PHE 0.054 0.001 PHE D 574 TYR 0.047 0.001 TYR C 162 ARG 0.008 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9185 (mtm) cc_final: 0.8898 (mtp) REVERT: A 176 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 294 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8085 (pt0) REVERT: A 368 LEU cc_start: 0.8230 (mm) cc_final: 0.7784 (mm) REVERT: A 442 MET cc_start: 0.8188 (tpp) cc_final: 0.7886 (tpp) REVERT: A 447 MET cc_start: 0.4027 (tpt) cc_final: 0.3751 (tpp) REVERT: A 485 MET cc_start: 0.7641 (tpt) cc_final: 0.7383 (tpp) REVERT: A 520 LEU cc_start: 0.3856 (pp) cc_final: 0.2967 (pp) REVERT: A 535 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 577 MET cc_start: 0.8547 (tmm) cc_final: 0.8278 (tmm) REVERT: A 578 MET cc_start: 0.5760 (tpt) cc_final: 0.5301 (tpp) REVERT: A 627 ASP cc_start: 0.9121 (m-30) cc_final: 0.8403 (t0) REVERT: A 643 ARG cc_start: 0.7494 (ptt180) cc_final: 0.7116 (ptt180) REVERT: A 702 TRP cc_start: 0.5281 (m100) cc_final: 0.5030 (m100) REVERT: E 28 ILE cc_start: 0.5797 (tp) cc_final: 0.5371 (tp) REVERT: E 37 MET cc_start: 0.6219 (mmm) cc_final: 0.5681 (tpt) REVERT: E 90 PHE cc_start: 0.7253 (t80) cc_final: 0.7017 (t80) REVERT: E 125 MET cc_start: 0.7348 (mtp) cc_final: 0.6940 (mmt) REVERT: E 128 GLU cc_start: 0.6918 (tt0) cc_final: 0.6599 (tt0) REVERT: B 91 ASN cc_start: 0.6548 (m-40) cc_final: 0.5974 (m-40) REVERT: B 159 LEU cc_start: 0.9047 (mm) cc_final: 0.8766 (mt) REVERT: B 211 PHE cc_start: 0.8416 (p90) cc_final: 0.8099 (p90) REVERT: B 294 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8628 (pt0) REVERT: B 447 MET cc_start: 0.5481 (tpt) cc_final: 0.4687 (ttt) REVERT: B 468 PHE cc_start: 0.8053 (m-80) cc_final: 0.7787 (m-80) REVERT: B 515 GLU cc_start: 0.8673 (tp30) cc_final: 0.7189 (mp0) REVERT: B 546 ASN cc_start: 0.7892 (m110) cc_final: 0.7367 (t0) REVERT: B 612 LEU cc_start: 0.8259 (mt) cc_final: 0.8008 (mt) REVERT: C 112 CYS cc_start: 0.2581 (t) cc_final: 0.1804 (t) REVERT: D 91 ASN cc_start: 0.6953 (m-40) cc_final: 0.6491 (m110) REVERT: D 162 TYR cc_start: 0.7981 (m-10) cc_final: 0.7666 (m-80) REVERT: D 474 MET cc_start: 0.7720 (ptt) cc_final: 0.7507 (ptm) REVERT: D 520 LEU cc_start: 0.4066 (pp) cc_final: 0.3461 (pp) REVERT: D 577 MET cc_start: 0.8430 (ttp) cc_final: 0.8217 (ttp) outliers start: 1 outliers final: 1 residues processed: 334 average time/residue: 0.2930 time to fit residues: 159.9794 Evaluate side-chains 265 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 144 GLN B 513 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS C 158 ASN C 418 GLN C 513 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21005 Z= 0.224 Angle : 0.637 10.950 28494 Z= 0.316 Chirality : 0.040 0.159 3236 Planarity : 0.004 0.051 3618 Dihedral : 4.311 19.482 2792 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.05 % Allowed : 0.90 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2538 helix: 1.28 (0.13), residues: 1596 sheet: -1.48 (0.52), residues: 68 loop : -1.42 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 702 HIS 0.009 0.001 HIS C 582 PHE 0.039 0.002 PHE B 531 TYR 0.024 0.001 TYR C 162 ARG 0.013 0.000 ARG D 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9167 (mtm) cc_final: 0.8929 (mtp) REVERT: A 176 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 215 MET cc_start: 0.9202 (tmm) cc_final: 0.8960 (tmm) REVERT: A 294 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8080 (pt0) REVERT: A 368 LEU cc_start: 0.8235 (mm) cc_final: 0.8021 (mm) REVERT: A 442 MET cc_start: 0.8103 (tpp) cc_final: 0.7772 (tpp) REVERT: A 520 LEU cc_start: 0.3837 (pp) cc_final: 0.2545 (pp) REVERT: A 535 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6306 (mt-10) REVERT: A 627 ASP cc_start: 0.9189 (m-30) cc_final: 0.8476 (t0) REVERT: A 643 ARG cc_start: 0.7391 (ptt180) cc_final: 0.6990 (ptt180) REVERT: A 702 TRP cc_start: 0.5276 (m100) cc_final: 0.4966 (m100) REVERT: E 37 MET cc_start: 0.6257 (mmm) cc_final: 0.5709 (tpt) REVERT: E 86 ILE cc_start: 0.6707 (mm) cc_final: 0.6281 (mm) REVERT: E 88 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8417 (mm-30) REVERT: E 125 MET cc_start: 0.7379 (mtp) cc_final: 0.7002 (mmt) REVERT: E 128 GLU cc_start: 0.6923 (tt0) cc_final: 0.6593 (tt0) REVERT: B 211 PHE cc_start: 0.8341 (p90) cc_final: 0.7986 (p90) REVERT: B 294 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8612 (pt0) REVERT: B 447 MET cc_start: 0.5685 (tpt) cc_final: 0.4922 (ttt) REVERT: B 468 PHE cc_start: 0.8131 (m-80) cc_final: 0.7833 (m-80) REVERT: B 515 GLU cc_start: 0.8711 (tp30) cc_final: 0.7173 (mp0) REVERT: B 546 ASN cc_start: 0.7848 (m110) cc_final: 0.7620 (t0) REVERT: C 129 ASN cc_start: 0.7927 (t0) cc_final: 0.7341 (t0) REVERT: C 447 MET cc_start: 0.5743 (mmm) cc_final: 0.5528 (mmm) REVERT: D 91 ASN cc_start: 0.7095 (m-40) cc_final: 0.6651 (m110) REVERT: D 162 TYR cc_start: 0.8166 (m-10) cc_final: 0.7908 (m-80) REVERT: D 474 MET cc_start: 0.7747 (ptt) cc_final: 0.7420 (ttp) REVERT: D 520 LEU cc_start: 0.4251 (pp) cc_final: 0.3589 (pp) REVERT: D 577 MET cc_start: 0.8446 (ttp) cc_final: 0.8222 (ttp) REVERT: D 622 GLU cc_start: 0.9287 (tt0) cc_final: 0.8838 (tp30) outliers start: 1 outliers final: 1 residues processed: 329 average time/residue: 0.2834 time to fit residues: 150.4781 Evaluate side-chains 254 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 253 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS B 513 GLN C 418 GLN C 513 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21005 Z= 0.185 Angle : 0.628 9.429 28494 Z= 0.307 Chirality : 0.039 0.210 3236 Planarity : 0.004 0.042 3618 Dihedral : 4.278 18.103 2792 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2538 helix: 1.31 (0.13), residues: 1590 sheet: -1.03 (0.58), residues: 60 loop : -1.37 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 702 HIS 0.008 0.001 HIS B 426 PHE 0.039 0.001 PHE B 531 TYR 0.022 0.001 TYR C 162 ARG 0.009 0.000 ARG D 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9161 (mtm) cc_final: 0.8866 (mtp) REVERT: A 162 TYR cc_start: 0.8667 (m-80) cc_final: 0.8266 (m-80) REVERT: A 176 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 442 MET cc_start: 0.8187 (tpp) cc_final: 0.7903 (tpp) REVERT: A 520 LEU cc_start: 0.3789 (pp) cc_final: 0.2527 (pp) REVERT: A 535 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6373 (mt-10) REVERT: A 627 ASP cc_start: 0.9229 (m-30) cc_final: 0.8513 (t0) REVERT: A 643 ARG cc_start: 0.7387 (ptt180) cc_final: 0.6869 (ptt180) REVERT: A 702 TRP cc_start: 0.5274 (m100) cc_final: 0.4836 (m100) REVERT: E 28 ILE cc_start: 0.5619 (tp) cc_final: 0.5260 (tp) REVERT: E 37 MET cc_start: 0.6254 (mmm) cc_final: 0.5715 (tpt) REVERT: E 86 ILE cc_start: 0.6582 (mm) cc_final: 0.6177 (mm) REVERT: E 88 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8477 (mm-30) REVERT: E 90 PHE cc_start: 0.6915 (t80) cc_final: 0.6592 (t80) REVERT: E 125 MET cc_start: 0.7359 (mtp) cc_final: 0.6969 (mmt) REVERT: E 128 GLU cc_start: 0.6921 (tt0) cc_final: 0.6576 (tt0) REVERT: B 91 ASN cc_start: 0.6331 (m-40) cc_final: 0.6003 (m-40) REVERT: B 159 LEU cc_start: 0.9074 (mm) cc_final: 0.8806 (mt) REVERT: B 211 PHE cc_start: 0.8293 (p90) cc_final: 0.7910 (p90) REVERT: B 260 MET cc_start: 0.8172 (tpp) cc_final: 0.7949 (tpp) REVERT: B 294 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8594 (pt0) REVERT: B 447 MET cc_start: 0.5684 (tpt) cc_final: 0.4950 (ttt) REVERT: B 515 GLU cc_start: 0.8717 (tp30) cc_final: 0.8082 (mm-30) REVERT: B 546 ASN cc_start: 0.7844 (m110) cc_final: 0.7514 (t0) REVERT: C 129 ASN cc_start: 0.7878 (t0) cc_final: 0.7391 (t0) REVERT: C 208 ASN cc_start: 0.7819 (p0) cc_final: 0.7522 (p0) REVERT: D 91 ASN cc_start: 0.7123 (m-40) cc_final: 0.6586 (m110) REVERT: D 162 TYR cc_start: 0.8244 (m-10) cc_final: 0.8004 (m-80) REVERT: D 474 MET cc_start: 0.7728 (ptt) cc_final: 0.7384 (ttp) REVERT: D 520 LEU cc_start: 0.4252 (pp) cc_final: 0.3593 (pp) REVERT: D 615 ARG cc_start: 0.8481 (mmm160) cc_final: 0.7686 (tpp-160) REVERT: D 622 GLU cc_start: 0.9281 (tt0) cc_final: 0.8812 (tp30) outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.3067 time to fit residues: 161.3304 Evaluate side-chains 258 residues out of total 2217 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 3.9990 chunk 214 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.0470 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 513 GLN C 418 GLN C 513 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.071714 restraints weight = 66655.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073479 restraints weight = 38299.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074522 restraints weight = 25438.184| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21005 Z= 0.149 Angle : 0.602 9.779 28494 Z= 0.293 Chirality : 0.038 0.160 3236 Planarity : 0.003 0.034 3618 Dihedral : 4.149 18.152 2792 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2538 helix: 1.43 (0.13), residues: 1580 sheet: -1.19 (0.50), residues: 72 loop : -1.24 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 702 HIS 0.007 0.001 HIS D 258 PHE 0.037 0.001 PHE B 531 TYR 0.013 0.001 TYR D 623 ARG 0.007 0.000 ARG D 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.75 seconds wall clock time: 75 minutes 6.57 seconds (4506.57 seconds total)