Starting phenix.real_space_refine on Fri Mar 15 11:29:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oge_20055/03_2024/6oge_20055_neut.pdb" } resolution = 4.36 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7189 2.51 5 N 1963 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11494 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4755 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 575} Chain breaks: 1 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1665 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.48, per 1000 atoms: 0.56 Number of scatterers: 11494 At special positions: 0 Unit cell: (116.49, 142.965, 145.083, 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 81 16.00 O 2261 8.00 N 1963 7.00 C 7189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 204 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 227 " distance=2.02 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 252 " distance=2.02 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.02 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 520 " distance=2.04 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 544 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 576 " distance=2.05 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 584 " distance=2.13 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 623 " distance=2.04 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A 634 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 642 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 68 " " NAG A 702 " - " ASN A 187 " " NAG A 707 " - " ASN A 571 " " NAG A 708 " - " ASN A 530 " " NAG A 709 " - " ASN A 629 " " NAG F 1 " - " ASN A 259 " Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 27 sheets defined 7.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.794A pdb=" N LEU A 46 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 4.089A pdb=" N ASP A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.960A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.117A pdb=" N CYS A 252 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.551A pdb=" N GLN A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 399 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 401 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.640A pdb=" N GLN A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 481 through 486 removed outlier: 4.418A pdb=" N PHE A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.691A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.976A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.776A pdb=" N ASP E 31 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.883A pdb=" N CYS A 26 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 102 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.038A pdb=" N LEU A 60 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA A 87 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU A 62 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 114 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN A 156 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 116 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 322 removed outlier: 3.965A pdb=" N ARG A 330 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 376 removed outlier: 6.346A pdb=" N LEU A 374 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 410 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLN A 446 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 412 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 465 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 555 removed outlier: 3.571A pdb=" N LEU A 561 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 removed outlier: 4.118A pdb=" N THR B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.351A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.552A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 85 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.891A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.866A pdb=" N TRP B 148 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.739A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 50 removed outlier: 6.474A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N MET C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR C 33 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.411A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.411A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AC2, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.988A pdb=" N THR D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.811A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AC5, first strand: chain 'D' and resid 62 through 63 Processing sheet with id=AC6, first strand: chain 'E' and resid 17 through 23 removed outlier: 4.076A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.546A pdb=" N ARG E 50 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AC9, first strand: chain 'E' and resid 149 through 152 removed outlier: 5.235A pdb=" N LYS E 150 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU E 185 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 152 " --> pdb=" O TYR E 183 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4474 1.38 - 1.55: 7163 1.55 - 1.71: 36 1.71 - 1.88: 91 1.88 - 2.04: 2 Bond restraints: 11766 Sorted by residual: bond pdb=" CB CYS A 584 " pdb=" SG CYS A 584 " ideal model delta sigma weight residual 1.808 2.042 -0.234 3.30e-02 9.18e+02 5.04e+01 bond pdb=" CA THR A 575 " pdb=" C THR A 575 " ideal model delta sigma weight residual 1.521 1.581 -0.060 1.38e-02 5.25e+03 1.87e+01 bond pdb=" N CYS A 576 " pdb=" CA CYS A 576 " ideal model delta sigma weight residual 1.463 1.509 -0.046 1.27e-02 6.20e+03 1.31e+01 bond pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " ideal model delta sigma weight residual 1.808 1.927 -0.119 3.30e-02 9.18e+02 1.30e+01 bond pdb=" C THR A 575 " pdb=" N CYS A 576 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.42e-02 4.96e+03 1.05e+01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 99.40 - 107.83: 738 107.83 - 116.26: 7482 116.26 - 124.69: 7506 124.69 - 133.12: 265 133.12 - 141.55: 24 Bond angle restraints: 16015 Sorted by residual: angle pdb=" CA CYS A 584 " pdb=" CB CYS A 584 " pdb=" SG CYS A 584 " ideal model delta sigma weight residual 114.40 141.55 -27.15 2.30e+00 1.89e-01 1.39e+02 angle pdb=" N ASP A 582 " pdb=" CA ASP A 582 " pdb=" C ASP A 582 " ideal model delta sigma weight residual 112.03 119.00 -6.97 1.31e+00 5.83e-01 2.83e+01 angle pdb=" C PRO A 606 " pdb=" N ASP A 607 " pdb=" CA ASP A 607 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C VAL D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" N CYS A 584 " pdb=" CA CYS A 584 " pdb=" CB CYS A 584 " ideal model delta sigma weight residual 110.07 117.31 -7.24 1.47e+00 4.63e-01 2.43e+01 ... (remaining 16010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 6965 22.63 - 45.27: 209 45.27 - 67.90: 26 67.90 - 90.53: 21 90.53 - 113.16: 18 Dihedral angle restraints: 7239 sinusoidal: 2950 harmonic: 4289 Sorted by residual: dihedral pdb=" CA HIS A 564 " pdb=" C HIS A 564 " pdb=" N PRO A 565 " pdb=" CA PRO A 565 " ideal model delta harmonic sigma weight residual -180.00 -138.33 -41.67 0 5.00e+00 4.00e-02 6.95e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 35.76 57.24 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA GLU E 155 " pdb=" C GLU E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 7236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1388 0.068 - 0.136: 381 0.136 - 0.204: 36 0.204 - 0.271: 3 0.271 - 0.339: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C2 NAG A 707 " pdb=" C1 NAG A 707 " pdb=" C3 NAG A 707 " pdb=" N2 NAG A 707 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ASP D 151 " pdb=" N ASP D 151 " pdb=" C ASP D 151 " pdb=" CB ASP D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1807 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 97 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 98 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 577 " -0.018 2.00e-02 2.50e+03 2.32e-02 9.38e+00 pdb=" CG PHE A 577 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 577 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 577 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 577 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 577 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 577 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 155 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO E 156 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " -0.040 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1340 2.74 - 3.28: 11128 3.28 - 3.82: 20476 3.82 - 4.36: 22846 4.36 - 4.90: 37301 Nonbonded interactions: 93091 Sorted by model distance: nonbonded pdb=" OD2 ASP D 185 " pdb=" OH TYR D 192 " model vdw 2.203 2.440 nonbonded pdb=" N ARG E 87 " pdb=" OD2 ASP E 90 " model vdw 2.235 2.520 nonbonded pdb=" O ASP B 82 " pdb=" OH TYR B 86 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR A 166 " pdb=" O SER A 202 " model vdw 2.264 2.440 nonbonded pdb=" O ASP C 86 " pdb=" OH TYR C 90 " model vdw 2.275 2.440 ... (remaining 93086 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 'B' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'D' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) } ncs_group { reference = (chain 'C' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) selection = (chain 'E' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 220)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.770 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.870 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.008 0.234 11766 Z= 0.548 Angle : 1.158 27.151 16015 Z= 0.617 Chirality : 0.058 0.339 1810 Planarity : 0.009 0.086 2074 Dihedral : 13.401 113.165 4393 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.54 % Favored : 86.39 % Rotamer: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 2.20 % 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: -4.34 (0.19), residues: 1477 helix: -4.66 (0.28), residues: 61 sheet: -2.57 (0.29), residues: 279 loop : -3.13 (0.16), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP E 161 HIS 0.015 0.003 HIS E 35 PHE 0.053 0.004 PHE A 577 TYR 0.043 0.004 TYR E 80 ARG 0.008 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8731 (mpm) cc_final: 0.8499 (mpm) REVERT: A 403 LEU cc_start: 0.9084 (tp) cc_final: 0.8734 (mp) REVERT: A 404 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 2 ILE cc_start: 0.9121 (mt) cc_final: 0.8778 (mm) REVERT: B 71 PHE cc_start: 0.8173 (m-10) cc_final: 0.7872 (m-10) REVERT: B 87 TYR cc_start: 0.8920 (m-80) cc_final: 0.8706 (m-80) REVERT: B 91 TYR cc_start: 0.8752 (p90) cc_final: 0.8533 (p90) REVERT: B 97 THR cc_start: 0.8862 (p) cc_final: 0.8598 (p) REVERT: B 105 GLU cc_start: 0.8045 (tp30) cc_final: 0.7672 (tp30) REVERT: B 106 ILE cc_start: 0.9608 (tt) cc_final: 0.9212 (tt) REVERT: B 122 ASP cc_start: 0.9545 (p0) cc_final: 0.9269 (t0) REVERT: B 129 THR cc_start: 0.9359 (p) cc_final: 0.9109 (p) REVERT: B 135 LEU cc_start: 0.9395 (tp) cc_final: 0.9033 (tp) REVERT: B 139 PHE cc_start: 0.9135 (p90) cc_final: 0.8460 (p90) REVERT: B 173 TYR cc_start: 0.8966 (m-80) cc_final: 0.8219 (m-80) REVERT: B 186 TYR cc_start: 0.8405 (t80) cc_final: 0.8059 (t80) REVERT: C 20 LEU cc_start: 0.8228 (mt) cc_final: 0.7982 (mt) REVERT: C 34 MET cc_start: 0.8776 (mmm) cc_final: 0.8458 (mmm) REVERT: C 79 TYR cc_start: 0.8115 (m-10) cc_final: 0.7424 (m-10) REVERT: C 90 TYR cc_start: 0.8039 (m-10) cc_final: 0.7756 (m-80) REVERT: C 100 PHE cc_start: 0.8093 (m-80) cc_final: 0.7646 (m-80) REVERT: C 142 VAL cc_start: 0.9598 (t) cc_final: 0.9309 (t) REVERT: C 178 LEU cc_start: 0.9489 (pp) cc_final: 0.9216 (pp) REVERT: C 199 ASN cc_start: 0.8025 (t0) cc_final: 0.7646 (t0) REVERT: C 201 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8850 (mmtt) REVERT: C 214 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8385 (mmmt) REVERT: D 139 PHE cc_start: 0.7938 (p90) cc_final: 0.7076 (p90) REVERT: D 140 TYR cc_start: 0.8635 (t80) cc_final: 0.8057 (t80) REVERT: D 168 SER cc_start: 0.8944 (p) cc_final: 0.8673 (t) REVERT: D 175 LEU cc_start: 0.9125 (tt) cc_final: 0.8916 (mp) REVERT: E 80 TYR cc_start: 0.8875 (m-80) cc_final: 0.8674 (m-10) REVERT: E 219 GLU cc_start: 0.8992 (pt0) cc_final: 0.8500 (tp30) outliers start: 2 outliers final: 1 residues processed: 307 average time/residue: 0.2940 time to fit residues: 120.2804 Evaluate side-chains 175 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.0570 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 111 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 155 GLN B 166 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 11766 Z= 0.294 Angle : 0.837 19.993 16015 Z= 0.430 Chirality : 0.048 0.222 1810 Planarity : 0.007 0.067 2074 Dihedral : 12.472 94.902 1788 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.20), residues: 1477 helix: -4.25 (0.37), residues: 51 sheet: -2.27 (0.28), residues: 306 loop : -2.73 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 110 HIS 0.009 0.001 HIS E 35 PHE 0.037 0.002 PHE C 99A TYR 0.035 0.002 TYR B 96 ARG 0.011 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9115 (pt0) cc_final: 0.8785 (pm20) REVERT: A 168 LEU cc_start: 0.9146 (tp) cc_final: 0.8939 (tt) REVERT: A 217 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8587 (tmm-80) REVERT: A 343 TYR cc_start: 0.8607 (m-80) cc_final: 0.8278 (m-10) REVERT: A 403 LEU cc_start: 0.9064 (tp) cc_final: 0.8779 (mt) REVERT: A 404 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 458 LEU cc_start: 0.9622 (tp) cc_final: 0.9322 (tt) REVERT: B 71 PHE cc_start: 0.8264 (m-10) cc_final: 0.7932 (m-10) REVERT: B 105 GLU cc_start: 0.8153 (tp30) cc_final: 0.7936 (tp30) REVERT: B 122 ASP cc_start: 0.9446 (p0) cc_final: 0.9195 (t0) REVERT: B 138 ASN cc_start: 0.9386 (m-40) cc_final: 0.9132 (m-40) REVERT: B 139 PHE cc_start: 0.9007 (p90) cc_final: 0.8151 (p90) REVERT: B 149 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9029 (mmtm) REVERT: B 155 GLN cc_start: 0.8440 (tp40) cc_final: 0.7429 (tm-30) REVERT: B 173 TYR cc_start: 0.8827 (m-80) cc_final: 0.8094 (m-80) REVERT: B 179 LEU cc_start: 0.9482 (tp) cc_final: 0.8839 (tp) REVERT: C 100 PHE cc_start: 0.8183 (m-80) cc_final: 0.7646 (m-80) REVERT: C 142 VAL cc_start: 0.9699 (t) cc_final: 0.9244 (t) REVERT: C 145 TYR cc_start: 0.7773 (p90) cc_final: 0.7480 (p90) REVERT: C 199 ASN cc_start: 0.7927 (t0) cc_final: 0.7703 (t0) REVERT: C 214 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8376 (mmmt) REVERT: D 139 PHE cc_start: 0.7623 (p90) cc_final: 0.7336 (p90) REVERT: D 140 TYR cc_start: 0.8482 (t80) cc_final: 0.7829 (t80) REVERT: E 30 LYS cc_start: 0.8544 (pptt) cc_final: 0.8135 (pptt) REVERT: E 50 ARG cc_start: 0.9353 (ttp-170) cc_final: 0.9003 (ttp-110) REVERT: E 136 LYS cc_start: 0.8165 (tptt) cc_final: 0.7959 (mmtt) outliers start: 2 outliers final: 1 residues processed: 243 average time/residue: 0.2744 time to fit residues: 92.2811 Evaluate side-chains 171 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 45 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 11766 Z= 0.237 Angle : 0.768 20.768 16015 Z= 0.391 Chirality : 0.047 0.238 1810 Planarity : 0.006 0.056 2074 Dihedral : 10.814 82.748 1788 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.24 % Favored : 88.63 % Rotamer: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.20), residues: 1477 helix: -3.97 (0.42), residues: 52 sheet: -2.19 (0.27), residues: 321 loop : -2.52 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 110 HIS 0.003 0.001 HIS D 198 PHE 0.047 0.002 PHE C 99A TYR 0.029 0.002 TYR B 96 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9008 (pt0) cc_final: 0.8792 (pm20) REVERT: A 343 TYR cc_start: 0.8557 (m-80) cc_final: 0.8264 (m-10) REVERT: A 403 LEU cc_start: 0.8924 (tp) cc_final: 0.8724 (mt) REVERT: A 458 LEU cc_start: 0.9605 (tp) cc_final: 0.9353 (tt) REVERT: B 71 PHE cc_start: 0.8244 (m-10) cc_final: 0.7896 (m-10) REVERT: B 98 PHE cc_start: 0.8240 (m-80) cc_final: 0.6740 (m-80) REVERT: B 139 PHE cc_start: 0.8884 (p90) cc_final: 0.7966 (p90) REVERT: B 148 TRP cc_start: 0.7041 (m100) cc_final: 0.5702 (m100) REVERT: B 149 LYS cc_start: 0.9286 (mtpp) cc_final: 0.8946 (mmtm) REVERT: B 155 GLN cc_start: 0.8328 (tp40) cc_final: 0.7476 (tm-30) REVERT: B 179 LEU cc_start: 0.9469 (tp) cc_final: 0.8624 (tp) REVERT: C 34 MET cc_start: 0.8867 (mmm) cc_final: 0.8123 (tpp) REVERT: C 92 CYS cc_start: 0.5853 (t) cc_final: 0.3677 (t) REVERT: C 100 PHE cc_start: 0.7876 (m-80) cc_final: 0.7494 (m-80) REVERT: C 142 VAL cc_start: 0.9732 (t) cc_final: 0.9244 (t) REVERT: C 145 TYR cc_start: 0.7634 (p90) cc_final: 0.7307 (p90) REVERT: C 214 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8355 (mmmt) REVERT: D 11 LEU cc_start: 0.9420 (mt) cc_final: 0.9212 (mt) REVERT: D 70 ASP cc_start: 0.9492 (m-30) cc_final: 0.8340 (m-30) REVERT: D 139 PHE cc_start: 0.7532 (p90) cc_final: 0.7230 (p90) REVERT: D 140 TYR cc_start: 0.8434 (t80) cc_final: 0.7765 (t80) REVERT: E 30 LYS cc_start: 0.8335 (pptt) cc_final: 0.7893 (pptt) REVERT: E 39 GLN cc_start: 0.8818 (tt0) cc_final: 0.8099 (tt0) REVERT: E 46 GLU cc_start: 0.9243 (tt0) cc_final: 0.8877 (pm20) outliers start: 2 outliers final: 1 residues processed: 243 average time/residue: 0.2629 time to fit residues: 87.8119 Evaluate side-chains 176 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 11766 Z= 0.334 Angle : 0.815 20.835 16015 Z= 0.410 Chirality : 0.047 0.233 1810 Planarity : 0.006 0.050 2074 Dihedral : 10.091 80.549 1788 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.00 % Favored : 86.87 % Rotamer: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.20), residues: 1477 helix: -3.90 (0.43), residues: 51 sheet: -2.07 (0.27), residues: 325 loop : -2.43 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 110 HIS 0.006 0.001 HIS B 189 PHE 0.048 0.002 PHE C 99A TYR 0.036 0.002 TYR B 96 ARG 0.007 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9486 (mm) cc_final: 0.8961 (mm) REVERT: A 75 GLN cc_start: 0.9067 (pt0) cc_final: 0.8863 (pm20) REVERT: A 141 GLN cc_start: 0.8475 (pt0) cc_final: 0.8186 (pp30) REVERT: A 343 TYR cc_start: 0.8494 (m-80) cc_final: 0.8172 (m-10) REVERT: A 403 LEU cc_start: 0.9015 (tp) cc_final: 0.8644 (mt) REVERT: A 458 LEU cc_start: 0.9659 (tp) cc_final: 0.9409 (tt) REVERT: B 71 PHE cc_start: 0.8254 (m-10) cc_final: 0.7973 (m-10) REVERT: B 105 GLU cc_start: 0.8079 (tp30) cc_final: 0.7846 (tp30) REVERT: B 106 ILE cc_start: 0.9611 (tt) cc_final: 0.9193 (tt) REVERT: B 139 PHE cc_start: 0.8933 (p90) cc_final: 0.7904 (p90) REVERT: B 145 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9090 (tppt) REVERT: B 149 LYS cc_start: 0.9235 (mtpp) cc_final: 0.8951 (mmtm) REVERT: B 155 GLN cc_start: 0.8251 (tp40) cc_final: 0.7229 (tm-30) REVERT: B 179 LEU cc_start: 0.9444 (tp) cc_final: 0.8815 (tp) REVERT: B 199 GLN cc_start: 0.8889 (tt0) cc_final: 0.8622 (tp40) REVERT: C 142 VAL cc_start: 0.9719 (t) cc_final: 0.9355 (t) REVERT: C 145 TYR cc_start: 0.7679 (p90) cc_final: 0.7253 (p90) REVERT: C 214 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8404 (mmmt) REVERT: D 11 LEU cc_start: 0.9453 (mt) cc_final: 0.9249 (mt) REVERT: D 139 PHE cc_start: 0.7567 (p90) cc_final: 0.6528 (p90) REVERT: D 140 TYR cc_start: 0.8374 (t80) cc_final: 0.7745 (t80) REVERT: D 175 LEU cc_start: 0.9167 (tt) cc_final: 0.8956 (mp) REVERT: E 30 LYS cc_start: 0.8419 (pptt) cc_final: 0.7969 (pptt) REVERT: E 46 GLU cc_start: 0.9237 (tt0) cc_final: 0.8843 (pm20) REVERT: E 50 ARG cc_start: 0.9115 (ttp-110) cc_final: 0.8606 (ttp-110) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.2522 time to fit residues: 73.9960 Evaluate side-chains 164 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.0670 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 11766 Z= 0.237 Angle : 0.751 20.688 16015 Z= 0.376 Chirality : 0.047 0.243 1810 Planarity : 0.005 0.062 2074 Dihedral : 9.242 75.122 1788 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.97 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.21), residues: 1477 helix: -3.60 (0.47), residues: 46 sheet: -1.84 (0.27), residues: 325 loop : -2.32 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 110 HIS 0.006 0.001 HIS D 198 PHE 0.054 0.002 PHE C 99A TYR 0.035 0.001 TYR B 96 ARG 0.010 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9097 (pt0) cc_final: 0.8873 (pm20) REVERT: A 343 TYR cc_start: 0.8449 (m-80) cc_final: 0.8159 (m-10) REVERT: A 403 LEU cc_start: 0.8892 (tp) cc_final: 0.8584 (mt) REVERT: B 71 PHE cc_start: 0.8257 (m-10) cc_final: 0.7953 (m-10) REVERT: B 97 THR cc_start: 0.8385 (p) cc_final: 0.8162 (p) REVERT: B 98 PHE cc_start: 0.8085 (m-80) cc_final: 0.7270 (m-80) REVERT: B 106 ILE cc_start: 0.9586 (tt) cc_final: 0.9113 (tt) REVERT: B 139 PHE cc_start: 0.8805 (p90) cc_final: 0.8173 (p90) REVERT: B 142 ARG cc_start: 0.9031 (tpt90) cc_final: 0.8756 (tpt90) REVERT: B 145 LYS cc_start: 0.9397 (mmpt) cc_final: 0.9104 (tppt) REVERT: B 149 LYS cc_start: 0.9258 (mtpp) cc_final: 0.8952 (mmtm) REVERT: B 155 GLN cc_start: 0.8213 (tp40) cc_final: 0.7227 (tm-30) REVERT: B 179 LEU cc_start: 0.9435 (tp) cc_final: 0.8828 (tp) REVERT: C 142 VAL cc_start: 0.9731 (t) cc_final: 0.9351 (t) REVERT: C 145 TYR cc_start: 0.7741 (p90) cc_final: 0.7523 (p90) REVERT: C 214 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8454 (mmmt) REVERT: D 11 LEU cc_start: 0.9412 (mt) cc_final: 0.9187 (mt) REVERT: D 139 PHE cc_start: 0.7320 (p90) cc_final: 0.6494 (p90) REVERT: D 140 TYR cc_start: 0.8375 (t80) cc_final: 0.7670 (t80) REVERT: D 175 LEU cc_start: 0.9239 (tt) cc_final: 0.8966 (mp) REVERT: E 30 LYS cc_start: 0.8414 (pptt) cc_final: 0.7956 (pptt) REVERT: E 39 GLN cc_start: 0.9326 (tt0) cc_final: 0.8961 (tt0) REVERT: E 46 GLU cc_start: 0.9190 (tt0) cc_final: 0.8843 (pm20) REVERT: E 80 TYR cc_start: 0.8401 (m-10) cc_final: 0.8054 (m-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2679 time to fit residues: 79.6195 Evaluate side-chains 171 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN A 527 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 11766 Z= 0.305 Angle : 0.790 20.616 16015 Z= 0.393 Chirality : 0.048 0.235 1810 Planarity : 0.006 0.084 2074 Dihedral : 9.016 69.691 1788 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.59 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.21), residues: 1477 helix: -3.60 (0.47), residues: 46 sheet: -1.88 (0.28), residues: 315 loop : -2.26 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 99 HIS 0.038 0.002 HIS E 35 PHE 0.037 0.002 PHE C 99A TYR 0.029 0.002 TYR B 96 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9103 (pt0) cc_final: 0.8885 (pm20) REVERT: A 340 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7809 (ttp80) REVERT: A 403 LEU cc_start: 0.9007 (tp) cc_final: 0.8598 (mt) REVERT: A 405 GLU cc_start: 0.8518 (tp30) cc_final: 0.8298 (tp30) REVERT: B 33 VAL cc_start: 0.9191 (t) cc_final: 0.8672 (t) REVERT: B 71 PHE cc_start: 0.8288 (m-10) cc_final: 0.8062 (m-10) REVERT: B 105 GLU cc_start: 0.8048 (tp30) cc_final: 0.7768 (tp30) REVERT: B 106 ILE cc_start: 0.9582 (tt) cc_final: 0.9002 (tt) REVERT: B 139 PHE cc_start: 0.8915 (p90) cc_final: 0.8010 (p90) REVERT: B 142 ARG cc_start: 0.9086 (tpt90) cc_final: 0.8827 (tpt90) REVERT: B 145 LYS cc_start: 0.9403 (mmpt) cc_final: 0.9127 (tppt) REVERT: B 148 TRP cc_start: 0.7451 (m100) cc_final: 0.4944 (m100) REVERT: B 149 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8956 (mmtm) REVERT: B 155 GLN cc_start: 0.8168 (tp40) cc_final: 0.7262 (tm-30) REVERT: B 179 LEU cc_start: 0.9426 (tp) cc_final: 0.8657 (tp) REVERT: B 194 CYS cc_start: 0.4417 (p) cc_final: 0.3711 (t) REVERT: C 142 VAL cc_start: 0.9701 (t) cc_final: 0.9478 (m) REVERT: C 143 LYS cc_start: 0.8994 (tptp) cc_final: 0.8615 (tppt) REVERT: C 144 ASP cc_start: 0.8745 (m-30) cc_final: 0.8150 (m-30) REVERT: C 214 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8441 (mmmt) REVERT: D 139 PHE cc_start: 0.7365 (p90) cc_final: 0.6322 (p90) REVERT: D 140 TYR cc_start: 0.8295 (t80) cc_final: 0.7592 (t80) REVERT: E 30 LYS cc_start: 0.8288 (pptt) cc_final: 0.7910 (pptt) REVERT: E 98 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.6501 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2853 time to fit residues: 81.4679 Evaluate side-chains 166 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 0.1980 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 275 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 11766 Z= 0.332 Angle : 0.828 20.767 16015 Z= 0.410 Chirality : 0.048 0.239 1810 Planarity : 0.006 0.067 2074 Dihedral : 8.725 61.535 1788 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.66 % Favored : 87.27 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.21), residues: 1477 helix: -3.51 (0.49), residues: 52 sheet: -1.91 (0.28), residues: 319 loop : -2.26 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 99 HIS 0.019 0.002 HIS E 35 PHE 0.040 0.003 PHE C 99A TYR 0.029 0.002 TYR B 96 ARG 0.006 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9145 (pt0) cc_final: 0.8920 (pm20) REVERT: A 403 LEU cc_start: 0.8981 (tp) cc_final: 0.8526 (mt) REVERT: B 105 GLU cc_start: 0.8035 (tp30) cc_final: 0.7764 (tp30) REVERT: B 139 PHE cc_start: 0.8666 (p90) cc_final: 0.8029 (p90) REVERT: B 142 ARG cc_start: 0.9091 (tpt90) cc_final: 0.8791 (tpt90) REVERT: B 145 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9112 (tppt) REVERT: B 149 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8923 (mmtm) REVERT: B 155 GLN cc_start: 0.8078 (tp40) cc_final: 0.7019 (tm-30) REVERT: B 179 LEU cc_start: 0.9426 (tp) cc_final: 0.8807 (tp) REVERT: C 145 TYR cc_start: 0.7692 (p90) cc_final: 0.7355 (p90) REVERT: C 214 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8441 (mmmt) REVERT: D 140 TYR cc_start: 0.8267 (t80) cc_final: 0.7753 (t80) REVERT: E 30 LYS cc_start: 0.8314 (pptt) cc_final: 0.7893 (pptt) REVERT: E 98 ARG cc_start: 0.7747 (ptt-90) cc_final: 0.7428 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2625 time to fit residues: 70.0266 Evaluate side-chains 156 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2845 > 50: distance: 22 - 65: 24.673 distance: 33 - 69: 14.113 distance: 36 - 66: 23.045 distance: 56 - 60: 21.912 distance: 60 - 61: 20.559 distance: 61 - 62: 19.899 distance: 61 - 64: 14.520 distance: 62 - 63: 21.772 distance: 62 - 66: 17.873 distance: 64 - 65: 17.698 distance: 66 - 67: 14.232 distance: 67 - 68: 27.644 distance: 67 - 70: 34.141 distance: 68 - 69: 15.717 distance: 68 - 73: 24.435 distance: 70 - 71: 26.099 distance: 70 - 72: 23.751 distance: 73 - 74: 14.768 distance: 74 - 75: 11.674 distance: 74 - 77: 17.075 distance: 75 - 76: 20.201 distance: 75 - 80: 19.866 distance: 77 - 78: 18.159 distance: 77 - 79: 20.131 distance: 80 - 81: 32.847 distance: 81 - 82: 39.262 distance: 81 - 84: 16.988 distance: 82 - 83: 36.838 distance: 82 - 85: 10.208 distance: 85 - 86: 17.837 distance: 86 - 87: 13.700 distance: 86 - 89: 45.149 distance: 87 - 88: 12.920 distance: 87 - 91: 23.191 distance: 89 - 90: 15.127 distance: 90 - 155: 21.715 distance: 91 - 92: 22.397 distance: 91 - 97: 24.661 distance: 92 - 93: 14.466 distance: 92 - 95: 17.591 distance: 93 - 94: 36.153 distance: 93 - 98: 25.947 distance: 95 - 96: 17.625 distance: 96 - 97: 29.087 distance: 98 - 99: 16.365 distance: 99 - 100: 30.970 distance: 99 - 102: 16.806 distance: 100 - 101: 40.881 distance: 100 - 110: 22.330 distance: 102 - 103: 10.477 distance: 103 - 104: 16.395 distance: 103 - 105: 12.353 distance: 104 - 106: 25.382 distance: 105 - 107: 9.662 distance: 106 - 108: 7.795 distance: 107 - 108: 9.476 distance: 108 - 109: 15.231 distance: 110 - 111: 20.823 distance: 111 - 112: 8.406 distance: 111 - 114: 24.558 distance: 112 - 113: 18.485 distance: 112 - 118: 9.658 distance: 114 - 115: 8.816 distance: 115 - 116: 25.081 distance: 115 - 117: 28.333 distance: 118 - 119: 7.743 distance: 119 - 120: 10.581 distance: 119 - 122: 10.236 distance: 120 - 121: 7.395 distance: 120 - 130: 4.344 distance: 122 - 123: 13.252 distance: 123 - 124: 17.022 distance: 123 - 125: 15.085 distance: 124 - 126: 13.106 distance: 125 - 127: 6.334 distance: 126 - 128: 9.752 distance: 127 - 128: 9.680 distance: 128 - 129: 3.039 distance: 130 - 131: 7.302 distance: 131 - 132: 16.743 distance: 131 - 134: 8.587 distance: 132 - 133: 20.246 distance: 132 - 138: 10.902 distance: 134 - 135: 21.390 distance: 135 - 136: 20.334 distance: 135 - 137: 23.759