Starting phenix.real_space_refine on Mon Mar 18 03:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4c_22664/03_2024/7k4c_22664_neut_updated.pdb" } resolution = 3.78 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= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Br 5 7.06 5 S 160 5.16 5 C 12782 2.51 5 N 3335 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19744 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "D" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4903 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 2, '81F': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'81F': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'81F': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.21, per 1000 atoms: 0.52 Number of scatterers: 19744 At special positions: 0 Unit cell: (143.45, 143.45, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 5 34.99 Ca 2 19.99 S 160 16.00 O 3460 8.00 N 3335 7.00 C 12782 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: 7.62 Conformation dependent library (CDL) restraints added in 3.7 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 51.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.509A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.587A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.606A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.730A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.504A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.044A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.670A pdb=" N GLN A 214 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 219 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 220 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.607A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.523A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.675A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 348 removed outlier: 3.660A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.811A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.748A pdb=" N THR A 419 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 4.024A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 removed outlier: 3.535A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 491 through 511 removed outlier: 3.628A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.758A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.563A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 removed outlier: 3.720A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.233A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 removed outlier: 3.509A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 64 removed outlier: 3.587A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.607A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.729A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.504A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 4.046A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.670A pdb=" N GLN B 214 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 219 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 220 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.608A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.522A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.674A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 removed outlier: 3.659A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.811A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.749A pdb=" N THR B 419 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 4.023A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 removed outlier: 3.534A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'B' and resid 491 through 511 removed outlier: 3.628A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 498 " --> pdb=" O CYS B 494 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.758A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 567 removed outlier: 3.564A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.720A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.233A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.509A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.587A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.606A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 136 No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.730A pdb=" N ALA C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.504A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 4.045A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.670A pdb=" N GLN C 214 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 219 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 220 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.607A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.522A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.675A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.660A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.811A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.749A pdb=" N THR C 419 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 removed outlier: 4.023A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 467 removed outlier: 3.534A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 486 Processing helix chain 'C' and resid 491 through 511 removed outlier: 3.629A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 498 " --> pdb=" O CYS C 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 removed outlier: 3.758A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 567 removed outlier: 3.564A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 580 removed outlier: 3.721A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.234A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.509A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.586A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.606A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 136 No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.729A pdb=" N ALA D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.504A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 4.045A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 removed outlier: 4.670A pdb=" N GLN D 214 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 219 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 220 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.607A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.522A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.674A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 removed outlier: 3.660A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.811A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 395 " --> pdb=" O VAL D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 removed outlier: 3.749A pdb=" N THR D 419 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 removed outlier: 4.024A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 467 removed outlier: 3.535A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 486 Processing helix chain 'D' and resid 491 through 511 removed outlier: 3.628A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 removed outlier: 3.758A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 567 removed outlier: 3.563A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 580 removed outlier: 3.721A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.233A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 631 through 636 removed outlier: 3.723A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 631 through 636 removed outlier: 3.722A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 631 through 636 removed outlier: 3.723A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 631 through 636 removed outlier: 3.723A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 8.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6705 1.37 - 1.51: 6918 1.51 - 1.66: 6309 1.66 - 1.80: 210 1.80 - 1.94: 67 Bond restraints: 20209 Sorted by residual: bond pdb=" C21 81F D 701 " pdb=" C22 81F D 701 " ideal model delta sigma weight residual 1.385 1.526 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 81F C 701 " pdb=" C22 81F C 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F B 701 " pdb=" C22 81F B 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F A 701 " pdb=" C22 81F A 701 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 81F D 702 " pdb=" C22 81F D 702 " ideal model delta sigma weight residual 1.385 1.515 -0.130 2.00e-02 2.50e+03 4.26e+01 ... (remaining 20204 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.32: 456 105.32 - 112.57: 10273 112.57 - 119.81: 7480 119.81 - 127.05: 8937 127.05 - 134.29: 278 Bond angle restraints: 27424 Sorted by residual: angle pdb=" C TYR C 89 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C TYR D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C TYR A 89 " pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLN B 369 " pdb=" N GLN B 370 " pdb=" CA GLN B 370 " ideal model delta sigma weight residual 122.44 117.00 5.44 1.19e+00 7.06e-01 2.09e+01 ... (remaining 27419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 11326 16.96 - 33.91: 627 33.91 - 50.87: 139 50.87 - 67.82: 3 67.82 - 84.78: 38 Dihedral angle restraints: 12133 sinusoidal: 4985 harmonic: 7148 Sorted by residual: dihedral pdb=" CA SER A 112 " pdb=" C SER A 112 " pdb=" N GLU A 113 " pdb=" CA GLU A 113 " ideal model delta harmonic sigma weight residual 180.00 145.08 34.92 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA SER D 112 " pdb=" C SER D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual 180.00 145.14 34.86 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 12130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1993 0.051 - 0.102: 875 0.102 - 0.153: 193 0.153 - 0.204: 30 0.204 - 0.255: 11 Chirality restraints: 3102 Sorted by residual: chirality pdb=" C05 81F D 702 " pdb=" C04 81F D 702 " pdb=" C06 81F D 702 " pdb=" C08 81F D 702 " both_signs ideal model delta sigma weight residual False -2.52 -2.77 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C10 81F D 702 " pdb=" C07 81F D 702 " pdb=" C09 81F D 702 " pdb=" N01 81F D 702 " both_signs ideal model delta sigma weight residual False 2.33 2.58 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3099 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 476 " -0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO C 477 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 477 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.046 5.00e-02 4.00e+02 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6021 2.82 - 3.34: 19275 3.34 - 3.86: 30556 3.86 - 4.38: 35379 4.38 - 4.90: 56578 Nonbonded interactions: 147809 Sorted by model distance: nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR B 339 " pdb=" O THR B 392 " model vdw 2.297 2.440 nonbonded pdb=" O ILE A 204 " pdb=" ND2 ASN A 252 " model vdw 2.347 2.520 ... (remaining 147804 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 28 through 638 or resid 701)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 28 through 638 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 51.160 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.141 20209 Z= 0.600 Angle : 1.088 11.728 27424 Z= 0.579 Chirality : 0.058 0.255 3102 Planarity : 0.007 0.084 3454 Dihedral : 12.364 84.777 7517 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.37 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.34 (0.12), residues: 2436 helix: -3.53 (0.08), residues: 1304 sheet: -3.43 (0.51), residues: 68 loop : -3.45 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 613 HIS 0.012 0.002 HIS A 522 PHE 0.029 0.003 PHE A 468 TYR 0.025 0.003 TYR D 623 ARG 0.006 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9600 (pp) cc_final: 0.9014 (pp) REVERT: A 96 MET cc_start: 0.9311 (mmm) cc_final: 0.8681 (mmm) REVERT: A 99 MET cc_start: 0.9029 (mmp) cc_final: 0.8829 (mtp) REVERT: A 122 HIS cc_start: 0.9389 (m90) cc_final: 0.8575 (m90) REVERT: A 267 GLN cc_start: 0.8339 (tt0) cc_final: 0.8101 (tp40) REVERT: A 303 GLU cc_start: 0.8739 (tt0) cc_final: 0.8200 (tp30) REVERT: A 305 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7414 (mtt180) REVERT: A 332 LEU cc_start: 0.9399 (tp) cc_final: 0.9127 (tt) REVERT: A 383 ASP cc_start: 0.9169 (t0) cc_final: 0.8737 (m-30) REVERT: A 402 VAL cc_start: 0.9265 (p) cc_final: 0.8575 (p) REVERT: A 435 MET cc_start: 0.8824 (mmt) cc_final: 0.8011 (mmm) REVERT: A 440 MET cc_start: 0.8875 (tpt) cc_final: 0.8594 (tpp) REVERT: A 442 MET cc_start: 0.9316 (tpp) cc_final: 0.8623 (tpp) REVERT: A 444 LEU cc_start: 0.9467 (mp) cc_final: 0.9172 (mt) REVERT: A 515 GLU cc_start: 0.7496 (tp30) cc_final: 0.7265 (mm-30) REVERT: A 587 HIS cc_start: 0.8857 (p-80) cc_final: 0.8201 (p-80) REVERT: A 588 GLU cc_start: 0.9061 (tt0) cc_final: 0.8781 (tt0) REVERT: A 590 ASP cc_start: 0.8562 (m-30) cc_final: 0.8077 (p0) REVERT: A 603 MET cc_start: 0.8829 (ttt) cc_final: 0.8475 (tmm) REVERT: B 92 LEU cc_start: 0.9615 (pp) cc_final: 0.9053 (pp) REVERT: B 96 MET cc_start: 0.9300 (mmm) cc_final: 0.8679 (mmm) REVERT: B 122 HIS cc_start: 0.9377 (m90) cc_final: 0.8590 (m90) REVERT: B 127 ASN cc_start: 0.9231 (t160) cc_final: 0.9028 (m-40) REVERT: B 267 GLN cc_start: 0.8383 (tt0) cc_final: 0.8114 (tp40) REVERT: B 303 GLU cc_start: 0.8772 (tt0) cc_final: 0.8136 (tm-30) REVERT: B 332 LEU cc_start: 0.9323 (tp) cc_final: 0.9036 (tt) REVERT: B 383 ASP cc_start: 0.9158 (t0) cc_final: 0.8710 (m-30) REVERT: B 386 LEU cc_start: 0.9376 (tp) cc_final: 0.9138 (mm) REVERT: B 402 VAL cc_start: 0.9293 (p) cc_final: 0.8688 (p) REVERT: B 435 MET cc_start: 0.8786 (mmt) cc_final: 0.8041 (mmt) REVERT: B 436 VAL cc_start: 0.9484 (t) cc_final: 0.9120 (p) REVERT: B 440 MET cc_start: 0.8793 (tpt) cc_final: 0.8503 (tpp) REVERT: B 441 VAL cc_start: 0.9659 (t) cc_final: 0.9411 (t) REVERT: B 442 MET cc_start: 0.9352 (tpp) cc_final: 0.8682 (tpp) REVERT: B 444 LEU cc_start: 0.9487 (mp) cc_final: 0.9182 (mt) REVERT: B 587 HIS cc_start: 0.8910 (p-80) cc_final: 0.8597 (p-80) REVERT: B 588 GLU cc_start: 0.9060 (tt0) cc_final: 0.8752 (tt0) REVERT: C 92 LEU cc_start: 0.9621 (pp) cc_final: 0.9060 (pp) REVERT: C 96 MET cc_start: 0.9303 (mmm) cc_final: 0.8721 (mmm) REVERT: C 122 HIS cc_start: 0.9387 (m90) cc_final: 0.8612 (m90) REVERT: C 127 ASN cc_start: 0.9220 (t160) cc_final: 0.8949 (m-40) REVERT: C 178 ILE cc_start: 0.9529 (mp) cc_final: 0.9255 (mp) REVERT: C 260 MET cc_start: 0.8946 (tpp) cc_final: 0.8742 (tpp) REVERT: C 279 ASP cc_start: 0.8888 (t70) cc_final: 0.8536 (t0) REVERT: C 303 GLU cc_start: 0.8771 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 305 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8324 (ttm-80) REVERT: C 323 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8489 (mmt180) REVERT: C 332 LEU cc_start: 0.9330 (tp) cc_final: 0.9030 (tt) REVERT: C 386 LEU cc_start: 0.9343 (tp) cc_final: 0.9117 (mm) REVERT: C 402 VAL cc_start: 0.9246 (p) cc_final: 0.8670 (p) REVERT: C 435 MET cc_start: 0.8890 (mmt) cc_final: 0.8296 (mmt) REVERT: C 440 MET cc_start: 0.8731 (tpt) cc_final: 0.8519 (tpp) REVERT: C 442 MET cc_start: 0.9342 (tpp) cc_final: 0.8745 (tpp) REVERT: C 485 MET cc_start: 0.8504 (ttm) cc_final: 0.7927 (ttm) REVERT: C 587 HIS cc_start: 0.8918 (p-80) cc_final: 0.8623 (p-80) REVERT: C 588 GLU cc_start: 0.9054 (tt0) cc_final: 0.8742 (tt0) REVERT: D 66 LYS cc_start: 0.9473 (tppt) cc_final: 0.9048 (tptp) REVERT: D 92 LEU cc_start: 0.9632 (pp) cc_final: 0.8956 (pp) REVERT: D 96 MET cc_start: 0.9254 (mmm) cc_final: 0.8532 (mmm) REVERT: D 99 MET cc_start: 0.8975 (mmp) cc_final: 0.8686 (mtt) REVERT: D 157 CYS cc_start: 0.9382 (m) cc_final: 0.8949 (t) REVERT: D 178 ILE cc_start: 0.9464 (mp) cc_final: 0.9206 (mp) REVERT: D 213 CYS cc_start: 0.9025 (t) cc_final: 0.8407 (t) REVERT: D 255 MET cc_start: 0.8702 (tpp) cc_final: 0.8185 (tpt) REVERT: D 274 THR cc_start: 0.8698 (m) cc_final: 0.8352 (m) REVERT: D 305 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7310 (mtt180) REVERT: D 318 SER cc_start: 0.9724 (t) cc_final: 0.9497 (p) REVERT: D 330 CYS cc_start: 0.9587 (m) cc_final: 0.9320 (m) REVERT: D 332 LEU cc_start: 0.9393 (tp) cc_final: 0.9105 (tt) REVERT: D 435 MET cc_start: 0.8879 (mmt) cc_final: 0.8201 (mmm) REVERT: D 440 MET cc_start: 0.8959 (tpt) cc_final: 0.8686 (tpp) REVERT: D 442 MET cc_start: 0.9396 (tpp) cc_final: 0.8729 (tpp) REVERT: D 444 LEU cc_start: 0.9523 (mp) cc_final: 0.9189 (mt) REVERT: D 452 VAL cc_start: 0.9460 (t) cc_final: 0.9229 (t) REVERT: D 456 PHE cc_start: 0.9186 (m-10) cc_final: 0.8718 (m-10) REVERT: D 485 MET cc_start: 0.8481 (ttm) cc_final: 0.7458 (ttm) REVERT: D 587 HIS cc_start: 0.8875 (p-80) cc_final: 0.8476 (p-80) REVERT: D 588 GLU cc_start: 0.8961 (tt0) cc_final: 0.8389 (tm-30) REVERT: D 590 ASP cc_start: 0.8673 (m-30) cc_final: 0.8359 (p0) REVERT: D 603 MET cc_start: 0.8816 (ttt) cc_final: 0.8565 (tmm) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.3083 time to fit residues: 274.4674 Evaluate side-chains 376 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 118 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 118 GLN B 127 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 464 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 127 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 483 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 483 GLN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20209 Z= 0.305 Angle : 0.776 10.287 27424 Z= 0.396 Chirality : 0.043 0.151 3102 Planarity : 0.005 0.068 3454 Dihedral : 10.014 89.760 2805 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.47 % Favored : 89.37 % Rotamer: Outliers : 2.74 % Allowed : 13.02 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.67 (0.15), residues: 2436 helix: -1.79 (0.12), residues: 1368 sheet: -3.00 (0.52), residues: 68 loop : -3.27 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.003 0.001 HIS A 258 PHE 0.019 0.001 PHE D 162 TYR 0.034 0.002 TYR C 324 ARG 0.004 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 396 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9478 (pp) cc_final: 0.9008 (pp) REVERT: A 96 MET cc_start: 0.9116 (mmm) cc_final: 0.8532 (mmp) REVERT: A 122 HIS cc_start: 0.9365 (m90) cc_final: 0.8657 (m90) REVERT: A 302 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.7043 (tpm170) REVERT: A 303 GLU cc_start: 0.8749 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 305 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8279 (mtm180) REVERT: A 383 ASP cc_start: 0.9076 (t0) cc_final: 0.8600 (m-30) REVERT: A 435 MET cc_start: 0.9042 (mmt) cc_final: 0.8196 (mmm) REVERT: A 440 MET cc_start: 0.8944 (tpt) cc_final: 0.8663 (tpp) REVERT: A 442 MET cc_start: 0.9061 (tpp) cc_final: 0.8628 (mmm) REVERT: A 444 LEU cc_start: 0.9562 (mp) cc_final: 0.9246 (mt) REVERT: A 515 GLU cc_start: 0.7326 (tp30) cc_final: 0.6873 (mm-30) REVERT: A 577 MET cc_start: 0.8893 (tpp) cc_final: 0.8602 (tpp) REVERT: A 578 MET cc_start: 0.8201 (mmt) cc_final: 0.7856 (mmt) REVERT: A 587 HIS cc_start: 0.8867 (p-80) cc_final: 0.8388 (p-80) REVERT: A 588 GLU cc_start: 0.9133 (tt0) cc_final: 0.8922 (tt0) REVERT: A 590 ASP cc_start: 0.8637 (m-30) cc_final: 0.8091 (p0) REVERT: A 603 MET cc_start: 0.8718 (ttt) cc_final: 0.8512 (tmm) REVERT: B 92 LEU cc_start: 0.9476 (pp) cc_final: 0.9014 (pp) REVERT: B 122 HIS cc_start: 0.9344 (m90) cc_final: 0.8616 (m90) REVERT: B 159 LEU cc_start: 0.9437 (tp) cc_final: 0.9080 (tt) REVERT: B 302 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7316 (tpp-160) REVERT: B 303 GLU cc_start: 0.8762 (tt0) cc_final: 0.8332 (tp30) REVERT: B 383 ASP cc_start: 0.9065 (t0) cc_final: 0.8536 (m-30) REVERT: B 435 MET cc_start: 0.9071 (mmt) cc_final: 0.8233 (mmm) REVERT: B 440 MET cc_start: 0.8865 (tpt) cc_final: 0.8567 (tpp) REVERT: B 442 MET cc_start: 0.9107 (tpp) cc_final: 0.8669 (mmm) REVERT: B 444 LEU cc_start: 0.9565 (mp) cc_final: 0.9249 (mt) REVERT: B 577 MET cc_start: 0.8856 (tpp) cc_final: 0.8648 (tpp) REVERT: B 587 HIS cc_start: 0.8890 (p-80) cc_final: 0.8350 (p-80) REVERT: B 588 GLU cc_start: 0.9074 (tt0) cc_final: 0.8872 (tt0) REVERT: B 590 ASP cc_start: 0.8719 (m-30) cc_final: 0.8111 (p0) REVERT: B 635 ASP cc_start: 0.8738 (t0) cc_final: 0.8536 (t0) REVERT: C 92 LEU cc_start: 0.9516 (pp) cc_final: 0.9057 (pp) REVERT: C 122 HIS cc_start: 0.9333 (m90) cc_final: 0.8632 (m90) REVERT: C 159 LEU cc_start: 0.9445 (tp) cc_final: 0.9100 (tt) REVERT: C 303 GLU cc_start: 0.8788 (tt0) cc_final: 0.8340 (tp30) REVERT: C 383 ASP cc_start: 0.9063 (t0) cc_final: 0.8541 (m-30) REVERT: C 435 MET cc_start: 0.9097 (mmt) cc_final: 0.8197 (mmt) REVERT: C 442 MET cc_start: 0.9127 (tpp) cc_final: 0.8730 (tpp) REVERT: C 587 HIS cc_start: 0.8921 (p-80) cc_final: 0.8361 (p-80) REVERT: C 588 GLU cc_start: 0.9059 (tt0) cc_final: 0.8854 (tt0) REVERT: C 590 ASP cc_start: 0.8741 (m-30) cc_final: 0.8101 (p0) REVERT: D 66 LYS cc_start: 0.9505 (tppt) cc_final: 0.9043 (tptp) REVERT: D 92 LEU cc_start: 0.9489 (pp) cc_final: 0.8979 (pp) REVERT: D 96 MET cc_start: 0.9041 (mmm) cc_final: 0.8374 (mmp) REVERT: D 159 LEU cc_start: 0.9341 (tp) cc_final: 0.9019 (tt) REVERT: D 178 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8765 (mp) REVERT: D 303 GLU cc_start: 0.8705 (tt0) cc_final: 0.8137 (tp30) REVERT: D 318 SER cc_start: 0.9754 (t) cc_final: 0.9501 (p) REVERT: D 383 ASP cc_start: 0.9035 (t0) cc_final: 0.8471 (m-30) REVERT: D 435 MET cc_start: 0.9012 (mmt) cc_final: 0.8124 (mmt) REVERT: D 440 MET cc_start: 0.9048 (tpt) cc_final: 0.8816 (tpp) REVERT: D 442 MET cc_start: 0.9175 (tpp) cc_final: 0.8733 (tmm) REVERT: D 444 LEU cc_start: 0.9572 (mp) cc_final: 0.9281 (mt) REVERT: D 466 MET cc_start: 0.9233 (mtt) cc_final: 0.8882 (mmt) REVERT: D 485 MET cc_start: 0.8370 (ttm) cc_final: 0.7726 (ttm) REVERT: D 578 MET cc_start: 0.8159 (mmt) cc_final: 0.7789 (mmt) REVERT: D 587 HIS cc_start: 0.8868 (p-80) cc_final: 0.8586 (p-80) REVERT: D 588 GLU cc_start: 0.9035 (tt0) cc_final: 0.8810 (tt0) REVERT: D 590 ASP cc_start: 0.8708 (m-30) cc_final: 0.8209 (p0) REVERT: D 603 MET cc_start: 0.8782 (ttt) cc_final: 0.8558 (tmm) REVERT: D 635 ASP cc_start: 0.8671 (t0) cc_final: 0.8291 (t0) outliers start: 58 outliers final: 30 residues processed: 429 average time/residue: 0.2939 time to fit residues: 200.3571 Evaluate side-chains 365 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 334 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 483 GLN A 522 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20209 Z= 0.177 Angle : 0.677 11.399 27424 Z= 0.337 Chirality : 0.041 0.150 3102 Planarity : 0.004 0.071 3454 Dihedral : 9.401 89.832 2805 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.02 % Allowed : 15.52 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.16), residues: 2436 helix: -0.96 (0.13), residues: 1340 sheet: -2.86 (0.55), residues: 68 loop : -3.24 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 613 HIS 0.003 0.001 HIS D 522 PHE 0.013 0.001 PHE C 468 TYR 0.023 0.001 TYR C 324 ARG 0.007 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 377 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9483 (pp) cc_final: 0.8986 (pp) REVERT: A 122 HIS cc_start: 0.9318 (m90) cc_final: 0.8659 (m90) REVERT: A 200 LEU cc_start: 0.9459 (mt) cc_final: 0.9255 (mt) REVERT: A 302 ARG cc_start: 0.8310 (tpp-160) cc_final: 0.8099 (tpp-160) REVERT: A 303 GLU cc_start: 0.8751 (tt0) cc_final: 0.8196 (tp30) REVERT: A 383 ASP cc_start: 0.9001 (t0) cc_final: 0.8529 (m-30) REVERT: A 440 MET cc_start: 0.8971 (tpt) cc_final: 0.8658 (tmm) REVERT: A 442 MET cc_start: 0.9042 (tpp) cc_final: 0.8645 (mmm) REVERT: A 444 LEU cc_start: 0.9539 (mp) cc_final: 0.9331 (mt) REVERT: A 474 MET cc_start: 0.8907 (tpp) cc_final: 0.8646 (tpp) REVERT: A 515 GLU cc_start: 0.7112 (tp30) cc_final: 0.6697 (mm-30) REVERT: A 528 MET cc_start: 0.8613 (tpp) cc_final: 0.8380 (tpp) REVERT: A 577 MET cc_start: 0.8821 (tpp) cc_final: 0.8614 (tpp) REVERT: A 587 HIS cc_start: 0.8808 (p-80) cc_final: 0.8261 (p-80) REVERT: A 590 ASP cc_start: 0.8600 (m-30) cc_final: 0.8075 (p0) REVERT: A 603 MET cc_start: 0.8745 (ttt) cc_final: 0.8490 (tmm) REVERT: A 635 ASP cc_start: 0.8682 (t0) cc_final: 0.8244 (t0) REVERT: B 92 LEU cc_start: 0.9455 (pp) cc_final: 0.9245 (pp) REVERT: B 122 HIS cc_start: 0.9322 (m90) cc_final: 0.8608 (m90) REVERT: B 303 GLU cc_start: 0.8755 (tt0) cc_final: 0.8269 (tp30) REVERT: B 383 ASP cc_start: 0.8974 (t0) cc_final: 0.8496 (m-30) REVERT: B 440 MET cc_start: 0.8986 (tpt) cc_final: 0.8624 (tmm) REVERT: B 442 MET cc_start: 0.9094 (tpp) cc_final: 0.8661 (mmm) REVERT: B 444 LEU cc_start: 0.9517 (mp) cc_final: 0.9315 (mt) REVERT: B 528 MET cc_start: 0.8713 (tpp) cc_final: 0.8474 (tpp) REVERT: B 577 MET cc_start: 0.8792 (tpp) cc_final: 0.8445 (tpp) REVERT: B 587 HIS cc_start: 0.8846 (p-80) cc_final: 0.8310 (p-80) REVERT: B 590 ASP cc_start: 0.8649 (m-30) cc_final: 0.7949 (p0) REVERT: B 635 ASP cc_start: 0.8659 (t0) cc_final: 0.8286 (t0) REVERT: C 122 HIS cc_start: 0.9340 (m90) cc_final: 0.8599 (m90) REVERT: C 259 LEU cc_start: 0.9257 (tp) cc_final: 0.8955 (tp) REVERT: C 302 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7380 (tpp-160) REVERT: C 383 ASP cc_start: 0.9001 (t0) cc_final: 0.8558 (m-30) REVERT: C 442 MET cc_start: 0.9176 (tpp) cc_final: 0.8438 (tpp) REVERT: C 515 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7707 (mp0) REVERT: C 578 MET cc_start: 0.8218 (mmt) cc_final: 0.7707 (mmt) REVERT: C 587 HIS cc_start: 0.8838 (p-80) cc_final: 0.8289 (p-80) REVERT: C 590 ASP cc_start: 0.8681 (m-30) cc_final: 0.7975 (p0) REVERT: D 29 TRP cc_start: 0.6940 (t-100) cc_final: 0.6506 (t60) REVERT: D 66 LYS cc_start: 0.9507 (tppt) cc_final: 0.9026 (tptp) REVERT: D 92 LEU cc_start: 0.9435 (pp) cc_final: 0.8958 (pp) REVERT: D 99 MET cc_start: 0.8579 (mtp) cc_final: 0.8314 (ptp) REVERT: D 122 HIS cc_start: 0.9365 (m90) cc_final: 0.8825 (m90) REVERT: D 318 SER cc_start: 0.9762 (t) cc_final: 0.9507 (p) REVERT: D 331 MET cc_start: 0.8450 (tpp) cc_final: 0.7798 (tmm) REVERT: D 332 LEU cc_start: 0.9062 (tp) cc_final: 0.8784 (tp) REVERT: D 383 ASP cc_start: 0.8941 (t0) cc_final: 0.8425 (m-30) REVERT: D 435 MET cc_start: 0.9008 (mmt) cc_final: 0.8175 (mmt) REVERT: D 440 MET cc_start: 0.9053 (tpt) cc_final: 0.8769 (tpp) REVERT: D 442 MET cc_start: 0.9215 (tpp) cc_final: 0.8844 (mmm) REVERT: D 444 LEU cc_start: 0.9538 (mp) cc_final: 0.9228 (mt) REVERT: D 466 MET cc_start: 0.9140 (mtt) cc_final: 0.8871 (mmt) REVERT: D 485 MET cc_start: 0.8377 (ttm) cc_final: 0.7425 (ttm) REVERT: D 528 MET cc_start: 0.8805 (tpp) cc_final: 0.8524 (tpp) REVERT: D 577 MET cc_start: 0.8655 (tpp) cc_final: 0.8304 (tpp) REVERT: D 578 MET cc_start: 0.8117 (mmt) cc_final: 0.7733 (mmt) REVERT: D 587 HIS cc_start: 0.8827 (p-80) cc_final: 0.8381 (p-80) REVERT: D 590 ASP cc_start: 0.8670 (m-30) cc_final: 0.8173 (p0) REVERT: D 603 MET cc_start: 0.8731 (ttt) cc_final: 0.8466 (tmm) REVERT: D 635 ASP cc_start: 0.8633 (t0) cc_final: 0.8257 (t0) outliers start: 64 outliers final: 30 residues processed: 415 average time/residue: 0.2576 time to fit residues: 172.7314 Evaluate side-chains 368 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 338 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 0.0370 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 149 optimal weight: 10.0000 chunk 222 optimal weight: 0.0670 chunk 235 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 464 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 201 HIS C 464 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20209 Z= 0.150 Angle : 0.672 11.772 27424 Z= 0.325 Chirality : 0.041 0.164 3102 Planarity : 0.004 0.068 3454 Dihedral : 8.708 86.230 2805 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.36 % Allowed : 16.89 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2436 helix: -0.52 (0.14), residues: 1292 sheet: -2.72 (0.58), residues: 68 loop : -3.20 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 268 HIS 0.002 0.000 HIS D 587 PHE 0.026 0.001 PHE D 162 TYR 0.022 0.001 TYR C 324 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 398 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6967 (t-100) cc_final: 0.6551 (t60) REVERT: A 92 LEU cc_start: 0.9455 (pp) cc_final: 0.9229 (pp) REVERT: A 122 HIS cc_start: 0.9320 (m90) cc_final: 0.8689 (m90) REVERT: A 331 MET cc_start: 0.8474 (tpp) cc_final: 0.7616 (tmm) REVERT: A 383 ASP cc_start: 0.8986 (t0) cc_final: 0.8570 (m-30) REVERT: A 435 MET cc_start: 0.9041 (mmt) cc_final: 0.7959 (mmm) REVERT: A 440 MET cc_start: 0.8950 (tpt) cc_final: 0.8670 (tmm) REVERT: A 442 MET cc_start: 0.8950 (tpp) cc_final: 0.8624 (mmm) REVERT: A 444 LEU cc_start: 0.9528 (mp) cc_final: 0.9324 (mt) REVERT: A 474 MET cc_start: 0.8898 (tpp) cc_final: 0.8626 (tpp) REVERT: A 528 MET cc_start: 0.8597 (tpp) cc_final: 0.8217 (tpp) REVERT: A 577 MET cc_start: 0.8673 (tpp) cc_final: 0.8322 (tpp) REVERT: A 578 MET cc_start: 0.8181 (mmt) cc_final: 0.7934 (mmt) REVERT: A 587 HIS cc_start: 0.8724 (p-80) cc_final: 0.7807 (p-80) REVERT: A 590 ASP cc_start: 0.8533 (m-30) cc_final: 0.8169 (p0) REVERT: A 635 ASP cc_start: 0.8645 (t0) cc_final: 0.8218 (t0) REVERT: B 29 TRP cc_start: 0.6866 (t-100) cc_final: 0.6501 (t60) REVERT: B 122 HIS cc_start: 0.9307 (m90) cc_final: 0.8669 (m90) REVERT: B 242 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8970 (t) REVERT: B 290 GLN cc_start: 0.8621 (pp30) cc_final: 0.8070 (pp30) REVERT: B 302 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8227 (tpm170) REVERT: B 318 SER cc_start: 0.9773 (t) cc_final: 0.9568 (p) REVERT: B 331 MET cc_start: 0.8513 (tpp) cc_final: 0.7679 (tmm) REVERT: B 383 ASP cc_start: 0.8961 (t0) cc_final: 0.8492 (m-30) REVERT: B 435 MET cc_start: 0.9081 (mmt) cc_final: 0.8078 (mmm) REVERT: B 440 MET cc_start: 0.8969 (tpt) cc_final: 0.8692 (tmm) REVERT: B 442 MET cc_start: 0.9019 (tpp) cc_final: 0.8740 (mmm) REVERT: B 515 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7331 (mp0) REVERT: B 528 MET cc_start: 0.8698 (tpp) cc_final: 0.8357 (tpp) REVERT: B 577 MET cc_start: 0.8664 (tpp) cc_final: 0.8306 (tpp) REVERT: B 578 MET cc_start: 0.8307 (mmt) cc_final: 0.8020 (mmt) REVERT: B 587 HIS cc_start: 0.8762 (p-80) cc_final: 0.8521 (p-80) REVERT: C 29 TRP cc_start: 0.6914 (t-100) cc_final: 0.6576 (t60) REVERT: C 122 HIS cc_start: 0.9300 (m90) cc_final: 0.8660 (m90) REVERT: C 232 LEU cc_start: 0.8496 (tt) cc_final: 0.8282 (tp) REVERT: C 242 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9028 (t) REVERT: C 290 GLN cc_start: 0.8623 (pp30) cc_final: 0.8078 (pp30) REVERT: C 318 SER cc_start: 0.9766 (t) cc_final: 0.9549 (p) REVERT: C 331 MET cc_start: 0.8567 (tpp) cc_final: 0.7653 (tmm) REVERT: C 383 ASP cc_start: 0.8983 (t0) cc_final: 0.8457 (m-30) REVERT: C 435 MET cc_start: 0.9023 (mmt) cc_final: 0.8071 (mmm) REVERT: C 442 MET cc_start: 0.9141 (tpp) cc_final: 0.8776 (mmm) REVERT: C 454 MET cc_start: 0.9112 (tpp) cc_final: 0.8840 (tpp) REVERT: C 515 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7329 (mp0) REVERT: C 528 MET cc_start: 0.8751 (tpp) cc_final: 0.8469 (tpp) REVERT: C 577 MET cc_start: 0.8510 (tpp) cc_final: 0.8193 (tpp) REVERT: C 587 HIS cc_start: 0.8788 (p-80) cc_final: 0.8534 (p-80) REVERT: D 29 TRP cc_start: 0.6904 (t-100) cc_final: 0.6492 (t60) REVERT: D 66 LYS cc_start: 0.9499 (tppt) cc_final: 0.9052 (tptp) REVERT: D 92 LEU cc_start: 0.9386 (pp) cc_final: 0.8992 (pt) REVERT: D 281 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8787 (p) REVERT: D 318 SER cc_start: 0.9754 (t) cc_final: 0.9510 (p) REVERT: D 331 MET cc_start: 0.8558 (tpp) cc_final: 0.7804 (tmm) REVERT: D 383 ASP cc_start: 0.8874 (t0) cc_final: 0.8397 (m-30) REVERT: D 402 VAL cc_start: 0.9065 (p) cc_final: 0.8593 (p) REVERT: D 435 MET cc_start: 0.8984 (mmt) cc_final: 0.7950 (mmm) REVERT: D 440 MET cc_start: 0.9044 (tpt) cc_final: 0.8717 (tmm) REVERT: D 442 MET cc_start: 0.9105 (tpp) cc_final: 0.8790 (mmm) REVERT: D 444 LEU cc_start: 0.9520 (mp) cc_final: 0.9299 (mt) REVERT: D 466 MET cc_start: 0.9098 (mtt) cc_final: 0.8865 (mmt) REVERT: D 577 MET cc_start: 0.8475 (tpp) cc_final: 0.8157 (tpp) REVERT: D 603 MET cc_start: 0.8787 (ttt) cc_final: 0.8492 (tmm) REVERT: D 635 ASP cc_start: 0.8641 (t0) cc_final: 0.8231 (t0) outliers start: 50 outliers final: 26 residues processed: 426 average time/residue: 0.2701 time to fit residues: 184.7200 Evaluate side-chains 398 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 369 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 0.0770 chunk 59 optimal weight: 8.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 464 ASN C 522 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20209 Z= 0.225 Angle : 0.698 13.061 27424 Z= 0.339 Chirality : 0.042 0.166 3102 Planarity : 0.004 0.058 3454 Dihedral : 8.673 89.268 2805 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 4.01 % Allowed : 18.02 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2436 helix: -0.38 (0.14), residues: 1320 sheet: -2.75 (0.59), residues: 68 loop : -3.14 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 268 HIS 0.007 0.001 HIS D 587 PHE 0.018 0.001 PHE B 162 TYR 0.015 0.001 TYR C 324 ARG 0.005 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 369 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6994 (t-100) cc_final: 0.6591 (t60) REVERT: A 34 ASP cc_start: 0.9321 (m-30) cc_final: 0.9079 (m-30) REVERT: A 122 HIS cc_start: 0.9322 (m90) cc_final: 0.8617 (m90) REVERT: A 242 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9040 (t) REVERT: A 331 MET cc_start: 0.8505 (tpp) cc_final: 0.7679 (tmm) REVERT: A 383 ASP cc_start: 0.9026 (t0) cc_final: 0.8558 (m-30) REVERT: A 435 MET cc_start: 0.9113 (mmt) cc_final: 0.8036 (mmm) REVERT: A 440 MET cc_start: 0.9016 (tpt) cc_final: 0.8732 (tmm) REVERT: A 444 LEU cc_start: 0.9522 (mp) cc_final: 0.9291 (mt) REVERT: A 474 MET cc_start: 0.8985 (tpp) cc_final: 0.8684 (tpp) REVERT: A 515 GLU cc_start: 0.7257 (tp30) cc_final: 0.6797 (mm-30) REVERT: A 528 MET cc_start: 0.8729 (tpp) cc_final: 0.8326 (tpp) REVERT: A 577 MET cc_start: 0.8741 (tpp) cc_final: 0.8393 (tpp) REVERT: A 578 MET cc_start: 0.8340 (mmt) cc_final: 0.7926 (mmt) REVERT: A 635 ASP cc_start: 0.8664 (t0) cc_final: 0.8245 (t0) REVERT: B 29 TRP cc_start: 0.6951 (t-100) cc_final: 0.6561 (t60) REVERT: B 122 HIS cc_start: 0.9289 (m90) cc_final: 0.8618 (m90) REVERT: B 130 MET cc_start: 0.8764 (ptt) cc_final: 0.8440 (ptt) REVERT: B 242 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9001 (t) REVERT: B 290 GLN cc_start: 0.8756 (pp30) cc_final: 0.8433 (pp30) REVERT: B 318 SER cc_start: 0.9780 (t) cc_final: 0.9565 (p) REVERT: B 331 MET cc_start: 0.8536 (tpp) cc_final: 0.7712 (tmm) REVERT: B 383 ASP cc_start: 0.8951 (t0) cc_final: 0.8489 (m-30) REVERT: B 386 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 403 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 435 MET cc_start: 0.9069 (mmt) cc_final: 0.8103 (mmm) REVERT: B 440 MET cc_start: 0.9081 (tpt) cc_final: 0.8863 (tmm) REVERT: B 442 MET cc_start: 0.9078 (tpp) cc_final: 0.8720 (mmm) REVERT: B 528 MET cc_start: 0.8759 (tpp) cc_final: 0.8369 (tpp) REVERT: B 577 MET cc_start: 0.8695 (tpp) cc_final: 0.8404 (tpp) REVERT: B 578 MET cc_start: 0.8372 (mmt) cc_final: 0.7978 (mmt) REVERT: B 603 MET cc_start: 0.8577 (ppp) cc_final: 0.8331 (ppp) REVERT: B 635 ASP cc_start: 0.8632 (t0) cc_final: 0.8387 (t0) REVERT: C 29 TRP cc_start: 0.6921 (t-100) cc_final: 0.6613 (t60) REVERT: C 122 HIS cc_start: 0.9292 (m90) cc_final: 0.8626 (m90) REVERT: C 130 MET cc_start: 0.8668 (ptt) cc_final: 0.8369 (ptt) REVERT: C 200 LEU cc_start: 0.9507 (mt) cc_final: 0.9275 (mt) REVERT: C 232 LEU cc_start: 0.8564 (tt) cc_final: 0.8345 (tp) REVERT: C 242 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9072 (t) REVERT: C 281 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 290 GLN cc_start: 0.8736 (pp30) cc_final: 0.8359 (pp30) REVERT: C 302 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.7997 (tpm170) REVERT: C 318 SER cc_start: 0.9791 (t) cc_final: 0.9559 (p) REVERT: C 331 MET cc_start: 0.8579 (tpp) cc_final: 0.7704 (tmm) REVERT: C 383 ASP cc_start: 0.8970 (t0) cc_final: 0.8558 (m-30) REVERT: C 435 MET cc_start: 0.9089 (mmt) cc_final: 0.8051 (mmm) REVERT: C 442 MET cc_start: 0.9151 (tpp) cc_final: 0.8767 (mmm) REVERT: C 528 MET cc_start: 0.8763 (tpp) cc_final: 0.8432 (tpp) REVERT: C 577 MET cc_start: 0.8570 (tpp) cc_final: 0.8268 (tpp) REVERT: C 635 ASP cc_start: 0.8541 (t0) cc_final: 0.8134 (t0) REVERT: D 29 TRP cc_start: 0.6938 (t-100) cc_final: 0.6535 (t60) REVERT: D 66 LYS cc_start: 0.9509 (tppt) cc_final: 0.9057 (tptp) REVERT: D 96 MET cc_start: 0.9271 (ptp) cc_final: 0.8635 (mmp) REVERT: D 99 MET cc_start: 0.8592 (ptm) cc_final: 0.7802 (ptm) REVERT: D 100 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8446 (mm-30) REVERT: D 290 GLN cc_start: 0.8607 (pm20) cc_final: 0.8017 (mm-40) REVERT: D 318 SER cc_start: 0.9755 (t) cc_final: 0.9499 (p) REVERT: D 331 MET cc_start: 0.8597 (tpp) cc_final: 0.7877 (tmm) REVERT: D 383 ASP cc_start: 0.8878 (t0) cc_final: 0.8378 (m-30) REVERT: D 435 MET cc_start: 0.9004 (mmt) cc_final: 0.8182 (mmt) REVERT: D 440 MET cc_start: 0.9127 (tpt) cc_final: 0.8820 (tmm) REVERT: D 442 MET cc_start: 0.9093 (tpp) cc_final: 0.8753 (mmm) REVERT: D 444 LEU cc_start: 0.9531 (mp) cc_final: 0.9312 (mt) REVERT: D 466 MET cc_start: 0.9187 (mtt) cc_final: 0.8937 (mmm) REVERT: D 528 MET cc_start: 0.8826 (tpp) cc_final: 0.8582 (tpp) REVERT: D 577 MET cc_start: 0.8645 (tpp) cc_final: 0.8227 (tpp) REVERT: D 603 MET cc_start: 0.8878 (ttt) cc_final: 0.8451 (tmm) REVERT: D 635 ASP cc_start: 0.8668 (t0) cc_final: 0.8288 (t0) outliers start: 85 outliers final: 51 residues processed: 418 average time/residue: 0.2700 time to fit residues: 182.7366 Evaluate side-chains 400 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 343 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 0.0980 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20209 Z= 0.197 Angle : 0.707 10.937 27424 Z= 0.338 Chirality : 0.042 0.185 3102 Planarity : 0.004 0.058 3454 Dihedral : 8.328 87.080 2805 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.74 % Favored : 91.17 % Rotamer: Outliers : 3.68 % Allowed : 19.58 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.17), residues: 2436 helix: -0.26 (0.15), residues: 1320 sheet: -2.79 (0.58), residues: 68 loop : -3.06 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 268 HIS 0.005 0.000 HIS D 587 PHE 0.012 0.001 PHE B 162 TYR 0.019 0.001 TYR C 324 ARG 0.003 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 360 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6948 (t-100) cc_final: 0.6551 (t60) REVERT: A 99 MET cc_start: 0.8991 (ptp) cc_final: 0.8443 (ptp) REVERT: A 110 MET cc_start: 0.7877 (mtp) cc_final: 0.7005 (mmt) REVERT: A 118 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: A 122 HIS cc_start: 0.9289 (m90) cc_final: 0.8518 (m90) REVERT: A 242 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9049 (t) REVERT: A 290 GLN cc_start: 0.8779 (pp30) cc_final: 0.8502 (pp30) REVERT: A 331 MET cc_start: 0.8519 (tpp) cc_final: 0.7689 (tmm) REVERT: A 383 ASP cc_start: 0.9025 (t0) cc_final: 0.8552 (m-30) REVERT: A 435 MET cc_start: 0.9067 (mmt) cc_final: 0.8106 (mmm) REVERT: A 440 MET cc_start: 0.9023 (tpt) cc_final: 0.8731 (tmm) REVERT: A 444 LEU cc_start: 0.9532 (mp) cc_final: 0.9299 (mt) REVERT: A 474 MET cc_start: 0.8983 (tpp) cc_final: 0.8686 (tpp) REVERT: A 515 GLU cc_start: 0.7247 (tp30) cc_final: 0.6814 (mm-30) REVERT: A 528 MET cc_start: 0.8715 (tpp) cc_final: 0.8319 (tpp) REVERT: A 577 MET cc_start: 0.8686 (tpp) cc_final: 0.8340 (tpp) REVERT: A 578 MET cc_start: 0.8317 (mmt) cc_final: 0.7914 (mmt) REVERT: A 635 ASP cc_start: 0.8686 (t0) cc_final: 0.8251 (t0) REVERT: B 29 TRP cc_start: 0.6918 (t-100) cc_final: 0.6540 (t60) REVERT: B 99 MET cc_start: 0.9133 (ptp) cc_final: 0.8640 (ptp) REVERT: B 110 MET cc_start: 0.7604 (mtp) cc_final: 0.7207 (mmm) REVERT: B 122 HIS cc_start: 0.9257 (m90) cc_final: 0.8556 (m90) REVERT: B 130 MET cc_start: 0.8723 (ptt) cc_final: 0.8362 (ptt) REVERT: B 242 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8976 (t) REVERT: B 290 GLN cc_start: 0.8743 (pp30) cc_final: 0.8435 (pp30) REVERT: B 318 SER cc_start: 0.9783 (t) cc_final: 0.9565 (p) REVERT: B 331 MET cc_start: 0.8529 (tpp) cc_final: 0.7716 (tmm) REVERT: B 383 ASP cc_start: 0.8938 (t0) cc_final: 0.8573 (m-30) REVERT: B 435 MET cc_start: 0.9019 (mmt) cc_final: 0.8040 (mmm) REVERT: B 442 MET cc_start: 0.9051 (tpp) cc_final: 0.8683 (mmm) REVERT: B 528 MET cc_start: 0.8738 (tpp) cc_final: 0.8356 (tpp) REVERT: B 577 MET cc_start: 0.8704 (tpp) cc_final: 0.8367 (tpp) REVERT: B 578 MET cc_start: 0.8387 (mmt) cc_final: 0.7970 (mmt) REVERT: B 603 MET cc_start: 0.8571 (ppp) cc_final: 0.8261 (ppp) REVERT: B 635 ASP cc_start: 0.8648 (t0) cc_final: 0.8400 (t0) REVERT: C 29 TRP cc_start: 0.6900 (t-100) cc_final: 0.6603 (t60) REVERT: C 34 ASP cc_start: 0.9232 (m-30) cc_final: 0.9011 (m-30) REVERT: C 122 HIS cc_start: 0.9279 (m90) cc_final: 0.8592 (m90) REVERT: C 130 MET cc_start: 0.8594 (ptt) cc_final: 0.8272 (ptt) REVERT: C 232 LEU cc_start: 0.8589 (tt) cc_final: 0.8312 (tp) REVERT: C 242 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9062 (t) REVERT: C 281 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 290 GLN cc_start: 0.8762 (pp30) cc_final: 0.8458 (pp30) REVERT: C 302 ARG cc_start: 0.8425 (tpp-160) cc_final: 0.8042 (tpm170) REVERT: C 318 SER cc_start: 0.9790 (t) cc_final: 0.9557 (p) REVERT: C 331 MET cc_start: 0.8554 (tpp) cc_final: 0.7722 (tmm) REVERT: C 383 ASP cc_start: 0.8967 (t0) cc_final: 0.8515 (m-30) REVERT: C 435 MET cc_start: 0.9079 (mmt) cc_final: 0.8040 (mmm) REVERT: C 442 MET cc_start: 0.9104 (tpp) cc_final: 0.8735 (mmm) REVERT: C 454 MET cc_start: 0.9183 (tpp) cc_final: 0.8853 (tpp) REVERT: C 528 MET cc_start: 0.8758 (tpp) cc_final: 0.8398 (tpp) REVERT: C 577 MET cc_start: 0.8503 (tpp) cc_final: 0.8271 (tpp) REVERT: C 635 ASP cc_start: 0.8587 (t0) cc_final: 0.8166 (t0) REVERT: D 29 TRP cc_start: 0.6941 (t-100) cc_final: 0.6548 (t60) REVERT: D 96 MET cc_start: 0.9262 (ptp) cc_final: 0.8944 (ptp) REVERT: D 99 MET cc_start: 0.8642 (ptm) cc_final: 0.8162 (ptm) REVERT: D 290 GLN cc_start: 0.8560 (pm20) cc_final: 0.8093 (mm-40) REVERT: D 318 SER cc_start: 0.9753 (t) cc_final: 0.9506 (p) REVERT: D 331 MET cc_start: 0.8587 (tpp) cc_final: 0.7870 (tmm) REVERT: D 383 ASP cc_start: 0.8852 (t0) cc_final: 0.8368 (m-30) REVERT: D 403 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 435 MET cc_start: 0.8974 (mmt) cc_final: 0.7899 (mmt) REVERT: D 440 MET cc_start: 0.9132 (tpt) cc_final: 0.8883 (tmm) REVERT: D 442 MET cc_start: 0.9017 (tpp) cc_final: 0.8718 (mmm) REVERT: D 444 LEU cc_start: 0.9539 (mp) cc_final: 0.9327 (mt) REVERT: D 466 MET cc_start: 0.9216 (mtt) cc_final: 0.8921 (mmm) REVERT: D 528 MET cc_start: 0.8773 (tpp) cc_final: 0.8478 (tpp) REVERT: D 577 MET cc_start: 0.8538 (tpp) cc_final: 0.8107 (tpp) REVERT: D 603 MET cc_start: 0.8773 (ttt) cc_final: 0.8454 (tmm) REVERT: D 635 ASP cc_start: 0.8658 (t0) cc_final: 0.8284 (t0) outliers start: 78 outliers final: 53 residues processed: 402 average time/residue: 0.2541 time to fit residues: 167.4139 Evaluate side-chains 391 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 201 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20209 Z= 0.164 Angle : 0.700 10.837 27424 Z= 0.331 Chirality : 0.041 0.171 3102 Planarity : 0.004 0.055 3454 Dihedral : 7.576 84.930 2805 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.21 % Favored : 91.67 % Rotamer: Outliers : 2.59 % Allowed : 21.13 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2436 helix: -0.29 (0.14), residues: 1348 sheet: -2.85 (0.58), residues: 68 loop : -3.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 268 HIS 0.004 0.000 HIS D 587 PHE 0.009 0.001 PHE D 162 TYR 0.018 0.001 TYR C 324 ARG 0.011 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 361 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6976 (t-100) cc_final: 0.6584 (t60) REVERT: A 110 MET cc_start: 0.7953 (mtp) cc_final: 0.7113 (mmt) REVERT: A 122 HIS cc_start: 0.9249 (m90) cc_final: 0.8574 (m90) REVERT: A 130 MET cc_start: 0.8431 (ptt) cc_final: 0.7869 (ptt) REVERT: A 242 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9014 (t) REVERT: A 283 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 331 MET cc_start: 0.8501 (tpp) cc_final: 0.7679 (tmm) REVERT: A 383 ASP cc_start: 0.9009 (t0) cc_final: 0.8560 (m-30) REVERT: A 435 MET cc_start: 0.9032 (mmt) cc_final: 0.7957 (mmm) REVERT: A 440 MET cc_start: 0.8992 (tpt) cc_final: 0.8729 (tmm) REVERT: A 444 LEU cc_start: 0.9528 (mp) cc_final: 0.9317 (mt) REVERT: A 474 MET cc_start: 0.8973 (tpp) cc_final: 0.8680 (tpp) REVERT: A 515 GLU cc_start: 0.7202 (tp30) cc_final: 0.6805 (mm-30) REVERT: A 528 MET cc_start: 0.8592 (tpp) cc_final: 0.8149 (tpp) REVERT: A 577 MET cc_start: 0.8617 (tpp) cc_final: 0.8255 (tpp) REVERT: A 578 MET cc_start: 0.8452 (mmt) cc_final: 0.8042 (mmt) REVERT: A 608 LEU cc_start: 0.9422 (mp) cc_final: 0.9112 (tt) REVERT: A 635 ASP cc_start: 0.8663 (t0) cc_final: 0.8250 (t0) REVERT: B 29 TRP cc_start: 0.6925 (t-100) cc_final: 0.6533 (t60) REVERT: B 122 HIS cc_start: 0.9209 (m90) cc_final: 0.8526 (m90) REVERT: B 130 MET cc_start: 0.8615 (ptt) cc_final: 0.8273 (ptt) REVERT: B 242 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8908 (t) REVERT: B 302 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7892 (tpm170) REVERT: B 318 SER cc_start: 0.9781 (t) cc_final: 0.9558 (p) REVERT: B 331 MET cc_start: 0.8510 (tpp) cc_final: 0.7699 (tmm) REVERT: B 383 ASP cc_start: 0.9000 (t0) cc_final: 0.8425 (m-30) REVERT: B 435 MET cc_start: 0.9040 (mmt) cc_final: 0.7940 (mmm) REVERT: B 442 MET cc_start: 0.9013 (tpp) cc_final: 0.8692 (mmm) REVERT: B 528 MET cc_start: 0.8674 (tpp) cc_final: 0.8269 (tpp) REVERT: B 577 MET cc_start: 0.8655 (tpp) cc_final: 0.8321 (tpp) REVERT: B 608 LEU cc_start: 0.9426 (mp) cc_final: 0.9104 (tt) REVERT: B 635 ASP cc_start: 0.8627 (t0) cc_final: 0.8361 (t0) REVERT: C 29 TRP cc_start: 0.6863 (t-100) cc_final: 0.6551 (t60) REVERT: C 78 MET cc_start: 0.7578 (pmm) cc_final: 0.7313 (pmm) REVERT: C 110 MET cc_start: 0.7548 (mtp) cc_final: 0.7205 (mmm) REVERT: C 122 HIS cc_start: 0.9269 (m90) cc_final: 0.8540 (m90) REVERT: C 130 MET cc_start: 0.8503 (ptt) cc_final: 0.8137 (ptt) REVERT: C 242 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9023 (t) REVERT: C 302 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.8114 (tpm170) REVERT: C 318 SER cc_start: 0.9773 (t) cc_final: 0.9541 (p) REVERT: C 331 MET cc_start: 0.8534 (tpp) cc_final: 0.7707 (tmm) REVERT: C 383 ASP cc_start: 0.9000 (t0) cc_final: 0.8518 (m-30) REVERT: C 435 MET cc_start: 0.9068 (mmt) cc_final: 0.8108 (mmm) REVERT: C 442 MET cc_start: 0.9035 (tpp) cc_final: 0.8696 (mmm) REVERT: C 454 MET cc_start: 0.9222 (tpp) cc_final: 0.8902 (tpp) REVERT: C 515 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 528 MET cc_start: 0.8693 (tpp) cc_final: 0.8319 (tpp) REVERT: C 577 MET cc_start: 0.8530 (tpp) cc_final: 0.8196 (tpp) REVERT: C 635 ASP cc_start: 0.8571 (t0) cc_final: 0.8158 (t0) REVERT: D 29 TRP cc_start: 0.6926 (t-100) cc_final: 0.6548 (t60) REVERT: D 283 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7741 (mt) REVERT: D 318 SER cc_start: 0.9745 (t) cc_final: 0.9503 (p) REVERT: D 331 MET cc_start: 0.8512 (tpp) cc_final: 0.7799 (tmm) REVERT: D 383 ASP cc_start: 0.8839 (t0) cc_final: 0.8368 (m-30) REVERT: D 403 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7650 (tm-30) REVERT: D 435 MET cc_start: 0.8963 (mmt) cc_final: 0.7901 (mmt) REVERT: D 440 MET cc_start: 0.9118 (tpt) cc_final: 0.8884 (tmm) REVERT: D 442 MET cc_start: 0.8993 (tpp) cc_final: 0.8758 (mmm) REVERT: D 444 LEU cc_start: 0.9539 (mp) cc_final: 0.9332 (mt) REVERT: D 466 MET cc_start: 0.9215 (mtt) cc_final: 0.8876 (mmm) REVERT: D 577 MET cc_start: 0.8446 (tpp) cc_final: 0.7974 (tpp) REVERT: D 603 MET cc_start: 0.8778 (ttt) cc_final: 0.8426 (tmm) REVERT: D 635 ASP cc_start: 0.8645 (t0) cc_final: 0.8278 (t0) outliers start: 55 outliers final: 40 residues processed: 390 average time/residue: 0.2686 time to fit residues: 168.5516 Evaluate side-chains 388 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 343 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 10.0000 chunk 93 optimal weight: 0.0270 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20209 Z= 0.164 Angle : 0.729 12.618 27424 Z= 0.340 Chirality : 0.042 0.173 3102 Planarity : 0.004 0.053 3454 Dihedral : 7.079 79.811 2805 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.13 % Favored : 91.75 % Rotamer: Outliers : 2.45 % Allowed : 21.18 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 2436 helix: -0.30 (0.14), residues: 1352 sheet: -2.74 (0.60), residues: 68 loop : -3.01 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 268 HIS 0.003 0.000 HIS D 587 PHE 0.008 0.001 PHE D 162 TYR 0.019 0.001 TYR C 324 ARG 0.009 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 369 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7972 (mtp) cc_final: 0.7121 (mmt) REVERT: A 122 HIS cc_start: 0.9239 (m90) cc_final: 0.8554 (m90) REVERT: A 130 MET cc_start: 0.8364 (ptt) cc_final: 0.7831 (ptt) REVERT: A 242 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9020 (t) REVERT: A 283 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 331 MET cc_start: 0.8484 (tpp) cc_final: 0.7664 (tmm) REVERT: A 383 ASP cc_start: 0.9033 (t0) cc_final: 0.8575 (m-30) REVERT: A 435 MET cc_start: 0.9016 (mmt) cc_final: 0.7921 (mmm) REVERT: A 454 MET cc_start: 0.9012 (tpt) cc_final: 0.8775 (tpt) REVERT: A 515 GLU cc_start: 0.7163 (tp30) cc_final: 0.6795 (mm-30) REVERT: A 528 MET cc_start: 0.8601 (tpp) cc_final: 0.8137 (tpp) REVERT: A 577 MET cc_start: 0.8537 (tpp) cc_final: 0.8255 (tpp) REVERT: A 608 LEU cc_start: 0.9393 (mp) cc_final: 0.9058 (tt) REVERT: A 635 ASP cc_start: 0.8667 (t0) cc_final: 0.8249 (t0) REVERT: B 29 TRP cc_start: 0.6900 (t-100) cc_final: 0.6520 (t60) REVERT: B 96 MET cc_start: 0.9134 (ppp) cc_final: 0.8927 (pmm) REVERT: B 110 MET cc_start: 0.7828 (mtp) cc_final: 0.7495 (mmm) REVERT: B 122 HIS cc_start: 0.9197 (m90) cc_final: 0.8491 (m90) REVERT: B 130 MET cc_start: 0.8576 (ptt) cc_final: 0.8245 (ptt) REVERT: B 242 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8915 (t) REVERT: B 302 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7573 (tpp-160) REVERT: B 318 SER cc_start: 0.9784 (t) cc_final: 0.9553 (p) REVERT: B 331 MET cc_start: 0.8536 (tpp) cc_final: 0.7701 (tmm) REVERT: B 383 ASP cc_start: 0.8970 (t0) cc_final: 0.8628 (m-30) REVERT: B 435 MET cc_start: 0.8950 (mmt) cc_final: 0.7877 (mmm) REVERT: B 442 MET cc_start: 0.8998 (tpp) cc_final: 0.8670 (mmm) REVERT: B 464 ASN cc_start: 0.8777 (t0) cc_final: 0.8336 (t0) REVERT: B 528 MET cc_start: 0.8681 (tpp) cc_final: 0.8256 (tpp) REVERT: B 577 MET cc_start: 0.8530 (tpp) cc_final: 0.8219 (tpp) REVERT: B 608 LEU cc_start: 0.9381 (mp) cc_final: 0.9036 (tt) REVERT: C 29 TRP cc_start: 0.6874 (t-100) cc_final: 0.6560 (t60) REVERT: C 122 HIS cc_start: 0.9268 (m90) cc_final: 0.8567 (m90) REVERT: C 130 MET cc_start: 0.8403 (ptt) cc_final: 0.8142 (ptt) REVERT: C 242 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9000 (t) REVERT: C 302 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.8126 (tpm170) REVERT: C 318 SER cc_start: 0.9777 (t) cc_final: 0.9536 (p) REVERT: C 331 MET cc_start: 0.8525 (tpp) cc_final: 0.7703 (tmm) REVERT: C 383 ASP cc_start: 0.9022 (t0) cc_final: 0.8637 (m-30) REVERT: C 435 MET cc_start: 0.9073 (mmt) cc_final: 0.8019 (mmm) REVERT: C 442 MET cc_start: 0.9015 (tpp) cc_final: 0.8685 (mmm) REVERT: C 454 MET cc_start: 0.9213 (tpp) cc_final: 0.8887 (tpp) REVERT: C 515 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 528 MET cc_start: 0.8634 (tpp) cc_final: 0.8222 (tpp) REVERT: C 577 MET cc_start: 0.8510 (tpp) cc_final: 0.8166 (tpp) REVERT: C 635 ASP cc_start: 0.8565 (t0) cc_final: 0.8144 (t0) REVERT: D 29 TRP cc_start: 0.6940 (t-100) cc_final: 0.6552 (t60) REVERT: D 66 LYS cc_start: 0.9514 (tppt) cc_final: 0.9039 (tptp) REVERT: D 283 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7622 (mp) REVERT: D 290 GLN cc_start: 0.8496 (pm20) cc_final: 0.8047 (mm-40) REVERT: D 318 SER cc_start: 0.9747 (t) cc_final: 0.9498 (p) REVERT: D 331 MET cc_start: 0.8511 (tpp) cc_final: 0.7804 (tmm) REVERT: D 383 ASP cc_start: 0.8854 (t0) cc_final: 0.8393 (m-30) REVERT: D 435 MET cc_start: 0.8956 (mmt) cc_final: 0.7871 (mmt) REVERT: D 440 MET cc_start: 0.9100 (tpt) cc_final: 0.8893 (tmm) REVERT: D 442 MET cc_start: 0.8951 (tpp) cc_final: 0.8744 (mmm) REVERT: D 444 LEU cc_start: 0.9535 (mp) cc_final: 0.9321 (mt) REVERT: D 466 MET cc_start: 0.9202 (mtt) cc_final: 0.8870 (mmm) REVERT: D 528 MET cc_start: 0.8588 (tpp) cc_final: 0.8331 (tpp) REVERT: D 577 MET cc_start: 0.8326 (tpp) cc_final: 0.8125 (tpp) REVERT: D 603 MET cc_start: 0.8774 (ttt) cc_final: 0.8408 (tmm) REVERT: D 608 LEU cc_start: 0.9417 (mp) cc_final: 0.9111 (tt) REVERT: D 635 ASP cc_start: 0.8645 (t0) cc_final: 0.8256 (t0) outliers start: 52 outliers final: 41 residues processed: 397 average time/residue: 0.2495 time to fit residues: 161.2494 Evaluate side-chains 392 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 346 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20209 Z= 0.185 Angle : 0.751 14.899 27424 Z= 0.351 Chirality : 0.043 0.220 3102 Planarity : 0.004 0.050 3454 Dihedral : 6.796 75.178 2805 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.58 % Rotamer: Outliers : 2.64 % Allowed : 21.37 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2436 helix: -0.26 (0.14), residues: 1352 sheet: -2.74 (0.60), residues: 68 loop : -2.96 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 268 HIS 0.003 0.000 HIS B 73 PHE 0.007 0.001 PHE C 468 TYR 0.019 0.001 TYR C 324 ARG 0.012 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8746 (ptp) cc_final: 0.8531 (ptp) REVERT: A 130 MET cc_start: 0.8328 (ptt) cc_final: 0.7830 (ptt) REVERT: A 242 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9008 (t) REVERT: A 283 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7685 (mp) REVERT: A 331 MET cc_start: 0.8514 (tpp) cc_final: 0.7684 (tmm) REVERT: A 383 ASP cc_start: 0.9025 (t0) cc_final: 0.8550 (m-30) REVERT: A 435 MET cc_start: 0.9029 (mmt) cc_final: 0.7974 (mmm) REVERT: A 474 MET cc_start: 0.8917 (tpp) cc_final: 0.8659 (tpp) REVERT: A 515 GLU cc_start: 0.7223 (tp30) cc_final: 0.6843 (mm-30) REVERT: A 528 MET cc_start: 0.8625 (tpp) cc_final: 0.8166 (tpp) REVERT: A 577 MET cc_start: 0.8616 (tpp) cc_final: 0.8267 (tpp) REVERT: A 608 LEU cc_start: 0.9370 (mp) cc_final: 0.9042 (tt) REVERT: A 635 ASP cc_start: 0.8652 (t0) cc_final: 0.8229 (t0) REVERT: B 29 TRP cc_start: 0.6903 (t-100) cc_final: 0.6519 (t60) REVERT: B 110 MET cc_start: 0.7849 (mtp) cc_final: 0.7456 (mmm) REVERT: B 122 HIS cc_start: 0.9211 (m90) cc_final: 0.8532 (m90) REVERT: B 130 MET cc_start: 0.8616 (ptt) cc_final: 0.8250 (ptt) REVERT: B 242 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8919 (t) REVERT: B 283 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (mp) REVERT: B 302 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7708 (tpp-160) REVERT: B 318 SER cc_start: 0.9787 (t) cc_final: 0.9551 (p) REVERT: B 331 MET cc_start: 0.8547 (tpp) cc_final: 0.7718 (tmm) REVERT: B 383 ASP cc_start: 0.8990 (t0) cc_final: 0.8438 (m-30) REVERT: B 435 MET cc_start: 0.8947 (mmt) cc_final: 0.7916 (mmm) REVERT: B 442 MET cc_start: 0.9001 (tpp) cc_final: 0.8669 (mmm) REVERT: B 464 ASN cc_start: 0.8805 (t0) cc_final: 0.8367 (t0) REVERT: B 528 MET cc_start: 0.8722 (tpp) cc_final: 0.8300 (tpp) REVERT: B 577 MET cc_start: 0.8522 (tpp) cc_final: 0.8211 (tpp) REVERT: B 608 LEU cc_start: 0.9358 (mp) cc_final: 0.9013 (tt) REVERT: C 29 TRP cc_start: 0.6888 (t-100) cc_final: 0.6579 (t60) REVERT: C 110 MET cc_start: 0.7583 (mtp) cc_final: 0.7304 (mmm) REVERT: C 122 HIS cc_start: 0.9246 (m90) cc_final: 0.8554 (m90) REVERT: C 130 MET cc_start: 0.8469 (ptt) cc_final: 0.8168 (ptt) REVERT: C 242 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8996 (t) REVERT: C 302 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8129 (tpm170) REVERT: C 318 SER cc_start: 0.9782 (t) cc_final: 0.9539 (p) REVERT: C 331 MET cc_start: 0.8530 (tpp) cc_final: 0.7733 (tmm) REVERT: C 383 ASP cc_start: 0.9004 (t0) cc_final: 0.8552 (m-30) REVERT: C 435 MET cc_start: 0.9077 (mmt) cc_final: 0.8017 (mmm) REVERT: C 442 MET cc_start: 0.9025 (tpp) cc_final: 0.8688 (mmm) REVERT: C 454 MET cc_start: 0.9183 (tpp) cc_final: 0.8857 (tpp) REVERT: C 515 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 528 MET cc_start: 0.8741 (tpp) cc_final: 0.8347 (tpp) REVERT: C 577 MET cc_start: 0.8538 (tpp) cc_final: 0.8202 (tpp) REVERT: C 635 ASP cc_start: 0.8574 (t0) cc_final: 0.8153 (t0) REVERT: D 29 TRP cc_start: 0.6978 (t-100) cc_final: 0.6586 (t60) REVERT: D 130 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (ppp) REVERT: D 283 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7634 (mp) REVERT: D 318 SER cc_start: 0.9751 (t) cc_final: 0.9501 (p) REVERT: D 331 MET cc_start: 0.8521 (tpp) cc_final: 0.7817 (tmm) REVERT: D 383 ASP cc_start: 0.8953 (t0) cc_final: 0.8599 (m-30) REVERT: D 390 LEU cc_start: 0.9433 (mm) cc_final: 0.9171 (mm) REVERT: D 403 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 435 MET cc_start: 0.8967 (mmt) cc_final: 0.7902 (mmt) REVERT: D 442 MET cc_start: 0.8983 (tpp) cc_final: 0.8760 (mmm) REVERT: D 444 LEU cc_start: 0.9537 (mp) cc_final: 0.9336 (mt) REVERT: D 466 MET cc_start: 0.9223 (mtt) cc_final: 0.8871 (mmm) REVERT: D 528 MET cc_start: 0.8630 (tpp) cc_final: 0.8376 (tpp) REVERT: D 603 MET cc_start: 0.8788 (ttt) cc_final: 0.8417 (tmm) REVERT: D 635 ASP cc_start: 0.8612 (t0) cc_final: 0.8226 (t0) outliers start: 56 outliers final: 43 residues processed: 382 average time/residue: 0.2491 time to fit residues: 156.3867 Evaluate side-chains 396 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 346 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 0.0770 chunk 20 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20209 Z= 0.173 Angle : 0.766 15.483 27424 Z= 0.353 Chirality : 0.042 0.190 3102 Planarity : 0.004 0.050 3454 Dihedral : 6.449 70.964 2805 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.50 % Rotamer: Outliers : 2.17 % Allowed : 22.22 % Favored : 75.61 % 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: -2.14 (0.17), residues: 2436 helix: -0.30 (0.14), residues: 1364 sheet: -2.68 (0.60), residues: 68 loop : -2.96 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 268 HIS 0.002 0.000 HIS A 582 PHE 0.007 0.001 PHE D 468 TYR 0.020 0.001 TYR C 324 ARG 0.009 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 358 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7933 (mtp) cc_final: 0.7241 (mmt) REVERT: A 130 MET cc_start: 0.8188 (ptt) cc_final: 0.7679 (ptt) REVERT: A 242 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8976 (t) REVERT: A 283 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 331 MET cc_start: 0.8465 (tpp) cc_final: 0.7643 (tmm) REVERT: A 383 ASP cc_start: 0.9016 (t0) cc_final: 0.8558 (m-30) REVERT: A 435 MET cc_start: 0.8942 (mmt) cc_final: 0.7867 (mmt) REVERT: A 474 MET cc_start: 0.8931 (tpp) cc_final: 0.8626 (tpp) REVERT: A 490 LEU cc_start: 0.7577 (tt) cc_final: 0.7164 (tt) REVERT: A 515 GLU cc_start: 0.7134 (tp30) cc_final: 0.6782 (mm-30) REVERT: A 528 MET cc_start: 0.8603 (tpp) cc_final: 0.8131 (tpp) REVERT: A 577 MET cc_start: 0.8523 (tpp) cc_final: 0.8189 (tpp) REVERT: A 608 LEU cc_start: 0.9342 (mp) cc_final: 0.9023 (tt) REVERT: A 635 ASP cc_start: 0.8644 (t0) cc_final: 0.8234 (t0) REVERT: B 29 TRP cc_start: 0.6875 (t-100) cc_final: 0.6513 (t60) REVERT: B 110 MET cc_start: 0.7732 (mtp) cc_final: 0.7141 (mmt) REVERT: B 130 MET cc_start: 0.8573 (ptt) cc_final: 0.8221 (ptt) REVERT: B 242 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8904 (t) REVERT: B 283 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 290 GLN cc_start: 0.8545 (pm20) cc_final: 0.7991 (mm-40) REVERT: B 302 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7895 (tpp-160) REVERT: B 318 SER cc_start: 0.9783 (t) cc_final: 0.9543 (p) REVERT: B 331 MET cc_start: 0.8519 (tpp) cc_final: 0.7683 (tmm) REVERT: B 383 ASP cc_start: 0.8974 (t0) cc_final: 0.8612 (m-30) REVERT: B 435 MET cc_start: 0.8911 (mmt) cc_final: 0.7860 (mmm) REVERT: B 442 MET cc_start: 0.8981 (tpp) cc_final: 0.8681 (mmm) REVERT: B 464 ASN cc_start: 0.8728 (t0) cc_final: 0.8279 (t0) REVERT: B 515 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7024 (mp0) REVERT: B 528 MET cc_start: 0.8611 (tpp) cc_final: 0.8154 (tpp) REVERT: B 577 MET cc_start: 0.8425 (tpp) cc_final: 0.8145 (tpp) REVERT: B 608 LEU cc_start: 0.9326 (mp) cc_final: 0.9010 (tt) REVERT: C 29 TRP cc_start: 0.6873 (t-100) cc_final: 0.6572 (t60) REVERT: C 122 HIS cc_start: 0.9233 (m90) cc_final: 0.8541 (m90) REVERT: C 130 MET cc_start: 0.8442 (ptt) cc_final: 0.8138 (ptt) REVERT: C 242 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (t) REVERT: C 302 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8007 (tpm170) REVERT: C 318 SER cc_start: 0.9778 (t) cc_final: 0.9532 (p) REVERT: C 331 MET cc_start: 0.8524 (tpp) cc_final: 0.7707 (tmm) REVERT: C 383 ASP cc_start: 0.9007 (t0) cc_final: 0.8556 (m-30) REVERT: C 435 MET cc_start: 0.9072 (mmt) cc_final: 0.8030 (mmm) REVERT: C 442 MET cc_start: 0.9013 (tpp) cc_final: 0.8708 (mmm) REVERT: C 464 ASN cc_start: 0.8749 (t0) cc_final: 0.8281 (t0) REVERT: C 515 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7278 (mm-30) REVERT: C 528 MET cc_start: 0.8650 (tpp) cc_final: 0.8232 (tpp) REVERT: C 577 MET cc_start: 0.8470 (tpp) cc_final: 0.7843 (tpp) REVERT: C 635 ASP cc_start: 0.8576 (t0) cc_final: 0.8155 (t0) REVERT: D 29 TRP cc_start: 0.6957 (t-100) cc_final: 0.6570 (t60) REVERT: D 130 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8124 (ppp) REVERT: D 283 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7614 (mp) REVERT: D 290 GLN cc_start: 0.8464 (pm20) cc_final: 0.8055 (mm-40) REVERT: D 318 SER cc_start: 0.9750 (t) cc_final: 0.9505 (p) REVERT: D 331 MET cc_start: 0.8494 (tpp) cc_final: 0.7790 (tmm) REVERT: D 345 MET cc_start: 0.8774 (tpp) cc_final: 0.8534 (tpt) REVERT: D 383 ASP cc_start: 0.8990 (t0) cc_final: 0.8579 (m-30) REVERT: D 403 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 435 MET cc_start: 0.8935 (mmt) cc_final: 0.7908 (mmt) REVERT: D 466 MET cc_start: 0.9174 (mtt) cc_final: 0.8855 (mmm) REVERT: D 528 MET cc_start: 0.8571 (tpp) cc_final: 0.8307 (tpp) REVERT: D 603 MET cc_start: 0.8792 (ttt) cc_final: 0.8432 (tmm) REVERT: D 608 LEU cc_start: 0.9394 (mp) cc_final: 0.9109 (tt) outliers start: 46 outliers final: 34 residues processed: 383 average time/residue: 0.2485 time to fit residues: 157.1350 Evaluate side-chains 388 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 347 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.0020 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078995 restraints weight = 54248.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082263 restraints weight = 27060.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084548 restraints weight = 16825.024| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20209 Z= 0.173 Angle : 0.769 15.246 27424 Z= 0.355 Chirality : 0.043 0.192 3102 Planarity : 0.004 0.049 3454 Dihedral : 6.278 67.689 2805 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 2.12 % Allowed : 22.45 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2436 helix: -0.31 (0.14), residues: 1364 sheet: -2.62 (0.61), residues: 68 loop : -2.91 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 268 HIS 0.002 0.000 HIS A 582 PHE 0.009 0.001 PHE A 162 TYR 0.021 0.001 TYR C 324 ARG 0.008 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4216.67 seconds wall clock time: 77 minutes 9.68 seconds (4629.68 seconds total)