Starting phenix.real_space_refine on Fri Mar 15 02:55:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/03_2024/7npw_12524.pdb" } resolution = 3.99 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 732 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6381 2.51 5 N 1569 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 477": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9723 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3241 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3241 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3241 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.28, per 1000 atoms: 0.54 Number of scatterers: 9723 At special positions: 0 Unit cell: (126.17, 121.286, 83.842, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1713 8.00 N 1569 7.00 C 6381 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: 3.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 81.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.556A pdb=" N VAL A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.767A pdb=" N LEU A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 115 Proline residue: A 84 - end of helix removed outlier: 4.932A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix removed outlier: 3.723A pdb=" N ASP A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.864A pdb=" N PHE A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.555A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.650A pdb=" N PHE A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.670A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.820A pdb=" N PHE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.547A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.720A pdb=" N ASN A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.896A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.027A pdb=" N ILE A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.521A pdb=" N LEU A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.768A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 115 Proline residue: B 84 - end of helix removed outlier: 4.931A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Proline residue: B 98 - end of helix removed outlier: 3.724A pdb=" N ASP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.865A pdb=" N PHE B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.556A pdb=" N LEU B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.651A pdb=" N PHE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 removed outlier: 3.669A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 removed outlier: 3.819A pdb=" N PHE B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.546A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 391 " --> pdb=" O THR B 387 " (cutoff:3.500A) Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 402 through 417 removed outlier: 3.719A pdb=" N ASN B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.897A pdb=" N THR B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 464 through 470 removed outlier: 4.026A pdb=" N ILE B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.520A pdb=" N LEU B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 48 through 69 removed outlier: 3.767A pdb=" N LEU C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 115 Proline residue: C 84 - end of helix removed outlier: 4.931A pdb=" N LEU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 3.723A pdb=" N ASP C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.865A pdb=" N PHE C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.555A pdb=" N LEU C 246 " --> pdb=" O ASN C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.651A pdb=" N PHE C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 304 removed outlier: 3.669A pdb=" N VAL C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 363 removed outlier: 3.820A pdb=" N PHE C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA C 355 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.547A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 391 " --> pdb=" O THR C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 402 through 417 removed outlier: 3.720A pdb=" N ASN C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 removed outlier: 3.897A pdb=" N THR C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 459 Processing helix chain 'C' and resid 464 through 470 removed outlier: 4.025A pdb=" N ILE C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.520A pdb=" N LEU C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 477 " --> pdb=" O TRP C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.516A pdb=" N VAL A 238 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.517A pdb=" N VAL B 238 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.517A pdb=" N VAL C 238 " --> pdb=" O GLN C 189 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2124 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: 2.79 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3018 1.34 - 1.46: 1839 1.46 - 1.58: 4917 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 9885 Sorted by residual: bond pdb=" C ALA C 289 " pdb=" N PRO C 290 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.64e-01 bond pdb=" C ALA B 289 " pdb=" N PRO B 290 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.39e-01 bond pdb=" C ALA A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.19e-01 bond pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.75e-02 3.27e+03 7.81e-01 bond pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.75e-02 3.27e+03 7.66e-01 ... (remaining 9880 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.77: 249 106.77 - 113.57: 5707 113.57 - 120.37: 3859 120.37 - 127.18: 3547 127.18 - 133.98: 66 Bond angle restraints: 13428 Sorted by residual: angle pdb=" C ILE A 469 " pdb=" CA ILE A 469 " pdb=" CB ILE A 469 " ideal model delta sigma weight residual 111.37 107.02 4.35 1.68e+00 3.54e-01 6.71e+00 angle pdb=" C ILE C 469 " pdb=" CA ILE C 469 " pdb=" CB ILE C 469 " ideal model delta sigma weight residual 111.37 107.06 4.31 1.68e+00 3.54e-01 6.57e+00 angle pdb=" C ILE B 469 " pdb=" CA ILE B 469 " pdb=" CB ILE B 469 " ideal model delta sigma weight residual 111.37 107.09 4.28 1.68e+00 3.54e-01 6.50e+00 angle pdb=" CB MET B 89 " pdb=" CG MET B 89 " pdb=" SD MET B 89 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" CB MET A 89 " pdb=" CG MET A 89 " pdb=" SD MET A 89 " ideal model delta sigma weight residual 112.70 120.19 -7.49 3.00e+00 1.11e-01 6.23e+00 ... (remaining 13423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5373 18.00 - 35.99: 411 35.99 - 53.99: 72 53.99 - 71.99: 12 71.99 - 89.98: 9 Dihedral angle restraints: 5877 sinusoidal: 2226 harmonic: 3651 Sorted by residual: dihedral pdb=" CA GLN B 93 " pdb=" C GLN B 93 " pdb=" N MET B 94 " pdb=" CA MET B 94 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLN C 93 " pdb=" C GLN C 93 " pdb=" N MET C 94 " pdb=" CA MET C 94 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN A 93 " pdb=" C GLN A 93 " pdb=" N MET A 94 " pdb=" CA MET A 94 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 960 0.028 - 0.056: 445 0.056 - 0.085: 191 0.085 - 0.113: 81 0.113 - 0.141: 12 Chirality restraints: 1689 Sorted by residual: chirality pdb=" CB VAL A 471 " pdb=" CA VAL A 471 " pdb=" CG1 VAL A 471 " pdb=" CG2 VAL A 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CB VAL B 471 " pdb=" CA VAL B 471 " pdb=" CG1 VAL B 471 " pdb=" CG2 VAL B 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB VAL C 471 " pdb=" CA VAL C 471 " pdb=" CG1 VAL C 471 " pdb=" CG2 VAL C 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1686 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 373 " -0.010 2.00e-02 2.50e+03 9.92e-03 1.72e+00 pdb=" CG PHE A 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 373 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 373 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE B 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 373 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 373 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 373 " -0.010 2.00e-02 2.50e+03 9.70e-03 1.65e+00 pdb=" CG PHE C 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 373 " -0.001 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2577 2.81 - 3.33: 10837 3.33 - 3.86: 16117 3.86 - 4.38: 17040 4.38 - 4.90: 29648 Nonbonded interactions: 76219 Sorted by model distance: nonbonded pdb=" O LYS A 384 " pdb=" NH1 ARG A 388 " model vdw 2.290 2.520 nonbonded pdb=" O LYS B 384 " pdb=" NH1 ARG B 388 " model vdw 2.290 2.520 nonbonded pdb=" O LYS C 384 " pdb=" NH1 ARG C 388 " model vdw 2.290 2.520 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 372 " model vdw 2.295 2.440 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.295 2.440 ... (remaining 76214 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' selection = chain 'B' selection = chain 'C' } 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 13.260 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.003 0.022 9885 Z= 0.158 Angle : 0.673 7.505 13428 Z= 0.354 Chirality : 0.041 0.141 1689 Planarity : 0.004 0.030 1641 Dihedral : 13.765 89.984 3525 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1254 helix: 1.46 (0.17), residues: 945 sheet: -1.52 (0.79), residues: 48 loop : -2.10 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 346 HIS 0.001 0.000 HIS C 328 PHE 0.023 0.001 PHE A 373 TYR 0.017 0.001 TYR C 405 ARG 0.011 0.001 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8711 (m-10) cc_final: 0.8231 (t80) REVERT: A 288 TYR cc_start: 0.9215 (t80) cc_final: 0.8787 (t80) REVERT: A 451 MET cc_start: 0.9204 (mmp) cc_final: 0.8754 (mmp) REVERT: A 476 ASP cc_start: 0.7474 (m-30) cc_final: 0.7077 (t0) REVERT: B 80 TYR cc_start: 0.8565 (m-10) cc_final: 0.8080 (t80) REVERT: B 189 GLN cc_start: 0.7050 (mp-120) cc_final: 0.6827 (mp10) REVERT: B 288 TYR cc_start: 0.9303 (t80) cc_final: 0.9002 (t80) REVERT: B 451 MET cc_start: 0.9069 (mmp) cc_final: 0.8611 (mmp) REVERT: C 80 TYR cc_start: 0.8669 (m-10) cc_final: 0.8027 (t80) REVERT: C 108 MET cc_start: 0.9013 (mmm) cc_final: 0.8619 (tpp) REVERT: C 251 MET cc_start: 0.8225 (mtp) cc_final: 0.7982 (tmm) REVERT: C 307 MET cc_start: 0.6234 (tmm) cc_final: 0.6021 (tmm) REVERT: C 451 MET cc_start: 0.9136 (mmp) cc_final: 0.8645 (mmp) REVERT: C 476 ASP cc_start: 0.7366 (m-30) cc_final: 0.7049 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1637 time to fit residues: 62.6812 Evaluate side-chains 203 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.0570 chunk 114 optimal weight: 10.0000 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9885 Z= 0.172 Angle : 0.610 10.529 13428 Z= 0.307 Chirality : 0.040 0.136 1689 Planarity : 0.004 0.029 1641 Dihedral : 3.819 18.858 1344 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.56 % Allowed : 14.30 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1254 helix: 1.48 (0.16), residues: 975 sheet: -1.45 (0.82), residues: 48 loop : -2.23 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 473 HIS 0.001 0.000 HIS C 328 PHE 0.017 0.001 PHE B 83 TYR 0.020 0.001 TYR B 75 ARG 0.005 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8712 (m-10) cc_final: 0.8188 (t80) REVERT: A 168 ASP cc_start: 0.8729 (m-30) cc_final: 0.8520 (m-30) REVERT: A 177 MET cc_start: 0.8819 (ttp) cc_final: 0.8299 (ttm) REVERT: A 288 TYR cc_start: 0.9086 (t80) cc_final: 0.8682 (t80) REVERT: A 316 MET cc_start: 0.9371 (mmm) cc_final: 0.9132 (mtm) REVERT: A 336 LEU cc_start: 0.8566 (tt) cc_final: 0.8239 (pp) REVERT: A 451 MET cc_start: 0.9112 (mmp) cc_final: 0.8674 (mmp) REVERT: B 80 TYR cc_start: 0.8681 (m-10) cc_final: 0.8151 (t80) REVERT: B 251 MET cc_start: 0.7704 (tmm) cc_final: 0.7435 (tmm) REVERT: B 288 TYR cc_start: 0.9166 (t80) cc_final: 0.8768 (t80) REVERT: B 405 TYR cc_start: 0.8821 (t80) cc_final: 0.8514 (t80) REVERT: B 451 MET cc_start: 0.9020 (mmp) cc_final: 0.8380 (mmp) REVERT: C 80 TYR cc_start: 0.8685 (m-10) cc_final: 0.8085 (t80) REVERT: C 108 MET cc_start: 0.9028 (mmm) cc_final: 0.8534 (tpp) REVERT: C 177 MET cc_start: 0.8753 (mtt) cc_final: 0.8290 (ttp) REVERT: C 251 MET cc_start: 0.8376 (mtp) cc_final: 0.8104 (tmm) REVERT: C 286 MET cc_start: 0.9286 (mmp) cc_final: 0.8916 (tpp) REVERT: C 288 TYR cc_start: 0.8889 (t80) cc_final: 0.8633 (t80) REVERT: C 307 MET cc_start: 0.6108 (tmm) cc_final: 0.5690 (tmm) REVERT: C 336 LEU cc_start: 0.8518 (tt) cc_final: 0.8274 (pp) REVERT: C 451 MET cc_start: 0.9121 (mmp) cc_final: 0.8649 (mmp) outliers start: 27 outliers final: 20 residues processed: 228 average time/residue: 0.1683 time to fit residues: 56.9650 Evaluate side-chains 221 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9885 Z= 0.155 Angle : 0.591 10.814 13428 Z= 0.296 Chirality : 0.040 0.179 1689 Planarity : 0.004 0.030 1641 Dihedral : 3.716 16.639 1344 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.65 % Allowed : 17.99 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1254 helix: 1.51 (0.16), residues: 981 sheet: -1.45 (0.82), residues: 48 loop : -2.14 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 473 HIS 0.001 0.000 HIS A 328 PHE 0.020 0.001 PHE B 170 TYR 0.018 0.001 TYR C 75 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8742 (m-10) cc_final: 0.8218 (t80) REVERT: A 177 MET cc_start: 0.8832 (ttp) cc_final: 0.8319 (ttm) REVERT: A 251 MET cc_start: 0.7887 (tmm) cc_final: 0.7652 (tmm) REVERT: A 288 TYR cc_start: 0.9042 (t80) cc_final: 0.8830 (t80) REVERT: A 317 TYR cc_start: 0.9193 (t80) cc_final: 0.8955 (t80) REVERT: A 451 MET cc_start: 0.9137 (mmp) cc_final: 0.8588 (mmp) REVERT: B 80 TYR cc_start: 0.8622 (m-10) cc_final: 0.8083 (t80) REVERT: B 288 TYR cc_start: 0.9096 (t80) cc_final: 0.8698 (t80) REVERT: B 451 MET cc_start: 0.9034 (mmp) cc_final: 0.8525 (mmp) REVERT: C 80 TYR cc_start: 0.8768 (m-10) cc_final: 0.8149 (t80) REVERT: C 108 MET cc_start: 0.9010 (mmm) cc_final: 0.8757 (tpp) REVERT: C 286 MET cc_start: 0.9344 (mmp) cc_final: 0.8994 (tpp) REVERT: C 307 MET cc_start: 0.5986 (tmm) cc_final: 0.5749 (tmm) REVERT: C 336 LEU cc_start: 0.8646 (tt) cc_final: 0.8437 (pp) REVERT: C 405 TYR cc_start: 0.8761 (t80) cc_final: 0.8259 (t80) REVERT: C 451 MET cc_start: 0.9135 (mmp) cc_final: 0.8343 (mmp) outliers start: 28 outliers final: 20 residues processed: 230 average time/residue: 0.1703 time to fit residues: 57.8283 Evaluate side-chains 212 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 30.0000 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 0.0970 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9885 Z= 0.236 Angle : 0.626 10.830 13428 Z= 0.322 Chirality : 0.040 0.171 1689 Planarity : 0.004 0.040 1641 Dihedral : 3.854 17.423 1344 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.98 % Allowed : 21.21 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1254 helix: 1.40 (0.16), residues: 987 sheet: -1.64 (0.78), residues: 48 loop : -2.08 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 473 HIS 0.002 0.001 HIS A 328 PHE 0.019 0.002 PHE B 170 TYR 0.023 0.002 TYR C 288 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 192 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8740 (m-10) cc_final: 0.8225 (t80) REVERT: A 242 ASN cc_start: 0.9145 (t0) cc_final: 0.8799 (t0) REVERT: A 288 TYR cc_start: 0.9051 (t80) cc_final: 0.8663 (t80) REVERT: A 304 MET cc_start: 0.9457 (tmm) cc_final: 0.9050 (tmm) REVERT: A 405 TYR cc_start: 0.8912 (t80) cc_final: 0.8465 (t80) REVERT: A 451 MET cc_start: 0.9152 (mmp) cc_final: 0.8331 (mmp) REVERT: A 476 ASP cc_start: 0.7742 (m-30) cc_final: 0.7172 (p0) REVERT: B 80 TYR cc_start: 0.8675 (m-10) cc_final: 0.8250 (t80) REVERT: B 242 ASN cc_start: 0.9221 (t0) cc_final: 0.8925 (t0) REVERT: B 451 MET cc_start: 0.9077 (mmp) cc_final: 0.8387 (mmp) REVERT: B 468 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9313 (tp) REVERT: B 476 ASP cc_start: 0.7750 (m-30) cc_final: 0.7068 (p0) REVERT: C 80 TYR cc_start: 0.8776 (m-10) cc_final: 0.8283 (t80) REVERT: C 88 LEU cc_start: 0.9631 (tt) cc_final: 0.9407 (tt) REVERT: C 108 MET cc_start: 0.9025 (mmm) cc_final: 0.8816 (tpp) REVERT: C 242 ASN cc_start: 0.9130 (t0) cc_final: 0.8782 (t0) REVERT: C 286 MET cc_start: 0.9389 (mmp) cc_final: 0.9143 (tpt) REVERT: C 336 LEU cc_start: 0.8772 (tt) cc_final: 0.8524 (pp) REVERT: C 405 TYR cc_start: 0.8955 (t80) cc_final: 0.8638 (t80) REVERT: C 451 MET cc_start: 0.9126 (mmp) cc_final: 0.8336 (mmp) REVERT: C 476 ASP cc_start: 0.7563 (m-30) cc_final: 0.7063 (p0) outliers start: 42 outliers final: 29 residues processed: 216 average time/residue: 0.1700 time to fit residues: 54.1144 Evaluate side-chains 209 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9885 Z= 0.158 Angle : 0.621 10.953 13428 Z= 0.311 Chirality : 0.041 0.196 1689 Planarity : 0.004 0.034 1641 Dihedral : 3.835 20.096 1344 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.88 % Allowed : 22.54 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1254 helix: 1.46 (0.16), residues: 981 sheet: -1.77 (0.77), residues: 48 loop : -2.06 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 346 HIS 0.001 0.000 HIS A 146 PHE 0.019 0.001 PHE B 83 TYR 0.027 0.001 TYR B 288 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8759 (m-10) cc_final: 0.8250 (t80) REVERT: A 242 ASN cc_start: 0.9016 (t0) cc_final: 0.8785 (t0) REVERT: A 288 TYR cc_start: 0.9006 (t80) cc_final: 0.8577 (t80) REVERT: A 304 MET cc_start: 0.9433 (tmm) cc_final: 0.8642 (tmm) REVERT: A 425 GLN cc_start: 0.9204 (pp30) cc_final: 0.8996 (pp30) REVERT: A 451 MET cc_start: 0.9134 (mmp) cc_final: 0.8720 (mmp) REVERT: B 80 TYR cc_start: 0.8643 (m-10) cc_final: 0.8249 (t80) REVERT: B 177 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: B 242 ASN cc_start: 0.9099 (t0) cc_final: 0.8852 (t0) REVERT: B 405 TYR cc_start: 0.8784 (t80) cc_final: 0.8240 (t80) REVERT: B 451 MET cc_start: 0.9017 (mmp) cc_final: 0.8205 (mmp) REVERT: B 468 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9342 (tp) REVERT: B 476 ASP cc_start: 0.7595 (m-30) cc_final: 0.7015 (p0) REVERT: C 80 TYR cc_start: 0.8750 (m-10) cc_final: 0.8366 (t80) REVERT: C 86 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.9035 (pm20) REVERT: C 177 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: C 187 PHE cc_start: 0.9356 (p90) cc_final: 0.8809 (p90) REVERT: C 251 MET cc_start: 0.7832 (tmm) cc_final: 0.7437 (tmm) REVERT: C 316 MET cc_start: 0.9283 (mmm) cc_final: 0.9058 (mtm) REVERT: C 336 LEU cc_start: 0.8831 (tt) cc_final: 0.8553 (pp) REVERT: C 405 TYR cc_start: 0.8848 (t80) cc_final: 0.8481 (t80) REVERT: C 451 MET cc_start: 0.9108 (mmp) cc_final: 0.8249 (mmp) outliers start: 41 outliers final: 26 residues processed: 234 average time/residue: 0.1729 time to fit residues: 60.0566 Evaluate side-chains 220 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9885 Z= 0.322 Angle : 0.688 11.056 13428 Z= 0.359 Chirality : 0.042 0.184 1689 Planarity : 0.004 0.044 1641 Dihedral : 4.185 21.925 1344 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.79 % Allowed : 25.00 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1254 helix: 1.25 (0.16), residues: 984 sheet: -1.81 (0.78), residues: 48 loop : -2.06 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 287 HIS 0.003 0.001 HIS C 328 PHE 0.023 0.002 PHE A 83 TYR 0.021 0.002 TYR A 317 ARG 0.003 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8827 (m-10) cc_final: 0.8368 (t80) REVERT: A 93 GLN cc_start: 0.8507 (pp30) cc_final: 0.7895 (pp30) REVERT: A 94 MET cc_start: 0.8975 (ttm) cc_final: 0.8697 (ttm) REVERT: A 184 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8834 (mm-30) REVERT: A 288 TYR cc_start: 0.9013 (t80) cc_final: 0.8490 (t80) REVERT: A 304 MET cc_start: 0.9496 (tmm) cc_final: 0.8652 (tmm) REVERT: A 405 TYR cc_start: 0.9003 (t80) cc_final: 0.8675 (t80) REVERT: A 451 MET cc_start: 0.9134 (mmp) cc_final: 0.8289 (mmp) REVERT: A 476 ASP cc_start: 0.7916 (m-30) cc_final: 0.7226 (p0) REVERT: B 80 TYR cc_start: 0.8722 (m-10) cc_final: 0.8383 (t80) REVERT: B 242 ASN cc_start: 0.9120 (t0) cc_final: 0.8724 (t0) REVERT: B 405 TYR cc_start: 0.8929 (t80) cc_final: 0.8445 (t80) REVERT: B 451 MET cc_start: 0.9072 (mmp) cc_final: 0.8386 (mmp) REVERT: B 468 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9318 (tp) REVERT: B 476 ASP cc_start: 0.7925 (m-30) cc_final: 0.7191 (p0) REVERT: C 73 MET cc_start: 0.7917 (ptm) cc_final: 0.7711 (ppp) REVERT: C 80 TYR cc_start: 0.8739 (m-10) cc_final: 0.8341 (t80) REVERT: C 83 PHE cc_start: 0.8571 (t80) cc_final: 0.8202 (t80) REVERT: C 86 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: C 93 GLN cc_start: 0.8564 (pp30) cc_final: 0.8257 (pp30) REVERT: C 94 MET cc_start: 0.9007 (ttm) cc_final: 0.8739 (ttm) REVERT: C 184 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8744 (mm-30) REVERT: C 336 LEU cc_start: 0.8967 (tt) cc_final: 0.8760 (pp) REVERT: C 405 TYR cc_start: 0.9001 (t80) cc_final: 0.8796 (t80) REVERT: C 451 MET cc_start: 0.9107 (mmp) cc_final: 0.8481 (mmp) REVERT: C 476 ASP cc_start: 0.7737 (m-30) cc_final: 0.7111 (p0) outliers start: 40 outliers final: 31 residues processed: 223 average time/residue: 0.1704 time to fit residues: 56.2827 Evaluate side-chains 206 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9885 Z= 0.194 Angle : 0.681 12.053 13428 Z= 0.339 Chirality : 0.042 0.178 1689 Planarity : 0.004 0.039 1641 Dihedral : 4.121 24.064 1344 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.07 % Allowed : 27.18 % Favored : 68.75 % 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: 0.72 (0.23), residues: 1254 helix: 1.19 (0.16), residues: 978 sheet: -1.86 (0.78), residues: 48 loop : -1.98 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 473 HIS 0.001 0.000 HIS C 328 PHE 0.022 0.001 PHE B 170 TYR 0.020 0.001 TYR B 288 ARG 0.001 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8801 (m-10) cc_final: 0.8341 (t80) REVERT: A 93 GLN cc_start: 0.8654 (pp30) cc_final: 0.8080 (pp30) REVERT: A 184 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8580 (mm-30) REVERT: A 242 ASN cc_start: 0.8979 (t0) cc_final: 0.8730 (t0) REVERT: A 288 TYR cc_start: 0.8999 (t80) cc_final: 0.8418 (t80) REVERT: A 304 MET cc_start: 0.9476 (tmm) cc_final: 0.9040 (tmm) REVERT: A 405 TYR cc_start: 0.8874 (t80) cc_final: 0.8548 (t80) REVERT: A 451 MET cc_start: 0.9121 (mmp) cc_final: 0.8278 (mmp) REVERT: B 80 TYR cc_start: 0.8654 (m-10) cc_final: 0.8362 (t80) REVERT: B 177 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8558 (ttp) REVERT: B 242 ASN cc_start: 0.9083 (t0) cc_final: 0.8664 (t0) REVERT: B 316 MET cc_start: 0.9399 (mmm) cc_final: 0.9147 (mtm) REVERT: B 405 TYR cc_start: 0.8879 (t80) cc_final: 0.8385 (t80) REVERT: B 451 MET cc_start: 0.9071 (mmp) cc_final: 0.8217 (mmp) REVERT: B 468 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9338 (tp) REVERT: B 476 ASP cc_start: 0.7790 (m-30) cc_final: 0.7111 (p0) REVERT: C 80 TYR cc_start: 0.8718 (m-10) cc_final: 0.8358 (t80) REVERT: C 83 PHE cc_start: 0.8347 (t80) cc_final: 0.8009 (t80) REVERT: C 86 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.9038 (pm20) REVERT: C 93 GLN cc_start: 0.8677 (pp30) cc_final: 0.8336 (pp30) REVERT: C 94 MET cc_start: 0.8958 (ttm) cc_final: 0.8646 (ttm) REVERT: C 177 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8509 (ttp) REVERT: C 184 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8913 (mm-30) REVERT: C 251 MET cc_start: 0.7828 (tmm) cc_final: 0.7593 (tmm) REVERT: C 405 TYR cc_start: 0.8947 (t80) cc_final: 0.8730 (t80) REVERT: C 451 MET cc_start: 0.9095 (mmp) cc_final: 0.8313 (mmp) REVERT: C 476 ASP cc_start: 0.7656 (m-30) cc_final: 0.7085 (p0) outliers start: 43 outliers final: 30 residues processed: 230 average time/residue: 0.1803 time to fit residues: 60.7871 Evaluate side-chains 225 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 464 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 0.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9885 Z= 0.182 Angle : 0.706 11.247 13428 Z= 0.346 Chirality : 0.043 0.200 1689 Planarity : 0.004 0.037 1641 Dihedral : 4.063 23.981 1344 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.88 % Allowed : 28.31 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1254 helix: 1.19 (0.16), residues: 978 sheet: -1.82 (0.78), residues: 48 loop : -2.06 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 346 HIS 0.002 0.000 HIS C 328 PHE 0.014 0.001 PHE B 83 TYR 0.018 0.001 TYR B 75 ARG 0.001 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8769 (m-10) cc_final: 0.8351 (t80) REVERT: A 93 GLN cc_start: 0.8580 (pp30) cc_final: 0.8058 (pp30) REVERT: A 184 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 242 ASN cc_start: 0.8883 (t0) cc_final: 0.8681 (t0) REVERT: A 288 TYR cc_start: 0.8963 (t80) cc_final: 0.8437 (t80) REVERT: A 304 MET cc_start: 0.9441 (tmm) cc_final: 0.8988 (tmm) REVERT: A 405 TYR cc_start: 0.8612 (t80) cc_final: 0.8269 (t80) REVERT: A 451 MET cc_start: 0.9031 (mmp) cc_final: 0.8096 (mmp) REVERT: B 80 TYR cc_start: 0.8664 (m-10) cc_final: 0.8362 (t80) REVERT: B 83 PHE cc_start: 0.8355 (t80) cc_final: 0.8108 (t80) REVERT: B 177 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (ttp) REVERT: B 242 ASN cc_start: 0.9029 (t0) cc_final: 0.8677 (t0) REVERT: B 405 TYR cc_start: 0.8770 (t80) cc_final: 0.8303 (t80) REVERT: B 451 MET cc_start: 0.9060 (mmp) cc_final: 0.8186 (mmp) REVERT: B 468 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9265 (tp) REVERT: B 476 ASP cc_start: 0.7720 (m-30) cc_final: 0.7076 (p0) REVERT: C 80 TYR cc_start: 0.8673 (m-10) cc_final: 0.8368 (t80) REVERT: C 83 PHE cc_start: 0.8308 (t80) cc_final: 0.7957 (t80) REVERT: C 86 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: C 93 GLN cc_start: 0.8629 (pp30) cc_final: 0.8282 (pp30) REVERT: C 177 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8561 (ttp) REVERT: C 184 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8890 (mm-30) REVERT: C 336 LEU cc_start: 0.9119 (tt) cc_final: 0.8846 (pp) REVERT: C 405 TYR cc_start: 0.8918 (t80) cc_final: 0.8671 (t80) REVERT: C 451 MET cc_start: 0.9080 (mmp) cc_final: 0.8241 (mmp) outliers start: 41 outliers final: 31 residues processed: 228 average time/residue: 0.1758 time to fit residues: 58.9463 Evaluate side-chains 230 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 464 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 116 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9885 Z= 0.176 Angle : 0.720 10.561 13428 Z= 0.352 Chirality : 0.043 0.194 1689 Planarity : 0.004 0.035 1641 Dihedral : 4.105 23.731 1344 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.69 % Allowed : 28.31 % Favored : 67.99 % 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: 0.70 (0.23), residues: 1254 helix: 1.19 (0.16), residues: 969 sheet: -1.75 (0.79), residues: 48 loop : -1.95 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 473 HIS 0.002 0.001 HIS C 328 PHE 0.014 0.001 PHE A 83 TYR 0.022 0.001 TYR B 317 ARG 0.001 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8735 (m-10) cc_final: 0.8324 (t80) REVERT: A 93 GLN cc_start: 0.8605 (pp30) cc_final: 0.8097 (pp30) REVERT: A 184 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8418 (mm-30) REVERT: A 288 TYR cc_start: 0.8994 (t80) cc_final: 0.8342 (t80) REVERT: A 304 MET cc_start: 0.9415 (tmm) cc_final: 0.8620 (tmm) REVERT: A 405 TYR cc_start: 0.8657 (t80) cc_final: 0.8345 (t80) REVERT: A 451 MET cc_start: 0.9031 (mmp) cc_final: 0.8129 (mmp) REVERT: B 80 TYR cc_start: 0.8658 (m-10) cc_final: 0.8335 (t80) REVERT: B 177 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8483 (ttp) REVERT: B 242 ASN cc_start: 0.8990 (t0) cc_final: 0.8699 (t0) REVERT: B 405 TYR cc_start: 0.8731 (t80) cc_final: 0.8269 (t80) REVERT: B 451 MET cc_start: 0.9044 (mmp) cc_final: 0.8151 (mmp) REVERT: B 468 ILE cc_start: 0.9598 (OUTLIER) cc_final: 0.9253 (tp) REVERT: B 476 ASP cc_start: 0.7677 (m-30) cc_final: 0.7120 (p0) REVERT: C 80 TYR cc_start: 0.8620 (m-10) cc_final: 0.8353 (t80) REVERT: C 83 PHE cc_start: 0.8270 (t80) cc_final: 0.7963 (t80) REVERT: C 93 GLN cc_start: 0.8688 (pp30) cc_final: 0.8347 (pp30) REVERT: C 184 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8844 (mm-30) REVERT: C 405 TYR cc_start: 0.8866 (t80) cc_final: 0.8619 (t80) REVERT: C 451 MET cc_start: 0.9057 (mmp) cc_final: 0.8184 (mmp) outliers start: 39 outliers final: 35 residues processed: 226 average time/residue: 0.1685 time to fit residues: 56.1907 Evaluate side-chains 231 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 464 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9885 Z= 0.202 Angle : 0.728 10.238 13428 Z= 0.363 Chirality : 0.044 0.194 1689 Planarity : 0.004 0.036 1641 Dihedral : 4.148 25.300 1344 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.79 % Allowed : 28.79 % Favored : 67.42 % 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: 0.70 (0.23), residues: 1254 helix: 1.19 (0.16), residues: 966 sheet: -1.75 (0.79), residues: 48 loop : -1.90 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 473 HIS 0.002 0.001 HIS C 328 PHE 0.027 0.001 PHE A 83 TYR 0.017 0.001 TYR B 75 ARG 0.001 0.000 ARG C 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8759 (m-10) cc_final: 0.8342 (t80) REVERT: A 93 GLN cc_start: 0.8596 (pp30) cc_final: 0.8060 (pp30) REVERT: A 177 MET cc_start: 0.8840 (ttp) cc_final: 0.8436 (ttm) REVERT: A 184 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8774 (mm-30) REVERT: A 288 TYR cc_start: 0.8992 (t80) cc_final: 0.8463 (t80) REVERT: A 304 MET cc_start: 0.9353 (tmm) cc_final: 0.8944 (tmm) REVERT: A 405 TYR cc_start: 0.8731 (t80) cc_final: 0.8378 (t80) REVERT: A 451 MET cc_start: 0.9074 (mmp) cc_final: 0.8163 (mmp) REVERT: B 80 TYR cc_start: 0.8594 (m-10) cc_final: 0.8336 (t80) REVERT: B 168 ASP cc_start: 0.8989 (m-30) cc_final: 0.8515 (m-30) REVERT: B 177 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: B 242 ASN cc_start: 0.9005 (t0) cc_final: 0.8708 (t0) REVERT: B 405 TYR cc_start: 0.8728 (t80) cc_final: 0.8280 (t80) REVERT: B 451 MET cc_start: 0.9031 (mmp) cc_final: 0.8168 (mmp) REVERT: B 468 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9278 (tp) REVERT: B 476 ASP cc_start: 0.7637 (m-30) cc_final: 0.7068 (p0) REVERT: C 80 TYR cc_start: 0.8606 (m-10) cc_final: 0.8335 (t80) REVERT: C 93 GLN cc_start: 0.8708 (pp30) cc_final: 0.8386 (pp30) REVERT: C 177 MET cc_start: 0.8725 (ttp) cc_final: 0.8322 (ttm) REVERT: C 184 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 451 MET cc_start: 0.9072 (mmp) cc_final: 0.8412 (mmp) outliers start: 40 outliers final: 35 residues processed: 217 average time/residue: 0.1703 time to fit residues: 55.0423 Evaluate side-chains 225 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 464 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.100360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072442 restraints weight = 35239.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074554 restraints weight = 18240.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.075921 restraints weight = 12084.010| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9885 Z= 0.209 Angle : 0.733 10.420 13428 Z= 0.366 Chirality : 0.044 0.187 1689 Planarity : 0.004 0.036 1641 Dihedral : 4.212 27.667 1344 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.60 % Allowed : 29.36 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1254 helix: 1.17 (0.16), residues: 966 sheet: -1.57 (0.80), residues: 48 loop : -1.89 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 287 HIS 0.003 0.001 HIS A 328 PHE 0.028 0.001 PHE A 83 TYR 0.018 0.001 TYR B 288 ARG 0.002 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.17 seconds wall clock time: 38 minutes 26.26 seconds (2306.26 seconds total)