Starting phenix.real_space_refine on Tue Dec 31 09:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1m_32944/12_2024/7x1m_32944.cif" } resolution = 2.74 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= 0.079 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 6609 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 37 5.16 5 C 6249 2.51 5 N 1657 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1615 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "D" Number of atoms: 1637 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1659 Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.60, per 1000 atoms: 0.77 Number of scatterers: 9908 At special positions: 0 Unit cell: (85, 110.5, 169.15, 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 37 16.00 O 1965 8.00 N 1657 7.00 C 6249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 391 " - pdb=" SG CYS M 525 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN M 343 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 32 sheets defined 8.7% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.618A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.845A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.734A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.880A pdb=" N ASN C 32 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.799A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.881A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.599A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.587A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'M' and resid 338 through 343 removed outlier: 3.631A pdb=" N PHE M 342 " --> pdb=" O PHE M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 349 through 353 removed outlier: 3.665A pdb=" N TRP M 353 " --> pdb=" O VAL M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 Processing helix chain 'M' and resid 383 through 387 removed outlier: 3.561A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.891A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.534A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.379A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.379A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 92 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.362A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.362A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 139 removed outlier: 3.593A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 181 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.996A pdb=" N TYR C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.074A pdb=" N VAL C 106 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.537A pdb=" N LEU C 142 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 184 " --> pdb=" O CYS C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 128 removed outlier: 5.169A pdb=" N LYS C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 182 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.513A pdb=" N SER C 157 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C 198 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.575A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.769A pdb=" N GLN D 160 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.564A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 196 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.654A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY H 98 " --> pdb=" O ASP H 33 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.654A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY H 98 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.775A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.775A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 93 through 94 removed outlier: 3.743A pdb=" N ASN M 394 " --> pdb=" O GLU M 516 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'M' and resid 473 through 474 409 hydrogen bonds defined for protein. 1008 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: 3.72 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2195 1.33 - 1.46: 3389 1.46 - 1.59: 4512 1.59 - 1.72: 0 1.72 - 1.85: 46 Bond restraints: 10142 Sorted by residual: bond pdb=" C ASP H 33 " pdb=" O ASP H 33 " ideal model delta sigma weight residual 1.234 1.198 0.036 1.40e-02 5.10e+03 6.62e+00 bond pdb=" N LYS H 64 " pdb=" CA LYS H 64 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.31e-02 5.83e+03 5.51e+00 bond pdb=" C ASP H 33 " pdb=" N MET H 34 " ideal model delta sigma weight residual 1.331 1.301 0.030 1.33e-02 5.65e+03 5.21e+00 bond pdb=" CA ASP H 33 " pdb=" C ASP H 33 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.38e-02 5.25e+03 4.16e+00 bond pdb=" C LYS A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.88e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 13429 2.36 - 4.72: 328 4.72 - 7.08: 31 7.08 - 9.44: 4 9.44 - 11.80: 2 Bond angle restraints: 13794 Sorted by residual: angle pdb=" N ASP H 33 " pdb=" CA ASP H 33 " pdb=" C ASP H 33 " ideal model delta sigma weight residual 110.41 103.26 7.15 1.23e+00 6.61e-01 3.38e+01 angle pdb=" N TYR M 495 " pdb=" CA TYR M 495 " pdb=" C TYR M 495 " ideal model delta sigma weight residual 111.07 116.46 -5.39 1.07e+00 8.73e-01 2.53e+01 angle pdb=" N GLY C 44 " pdb=" CA GLY C 44 " pdb=" C GLY C 44 " ideal model delta sigma weight residual 112.08 116.25 -4.17 1.01e+00 9.80e-01 1.70e+01 angle pdb=" C VAL D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C SER M 494 " pdb=" N TYR M 495 " pdb=" CA TYR M 495 " ideal model delta sigma weight residual 120.44 125.46 -5.02 1.30e+00 5.92e-01 1.49e+01 ... (remaining 13789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5560 17.08 - 34.16: 409 34.16 - 51.24: 70 51.24 - 68.32: 12 68.32 - 85.40: 14 Dihedral angle restraints: 6065 sinusoidal: 2345 harmonic: 3720 Sorted by residual: dihedral pdb=" CA GLU A 162 " pdb=" C GLU A 162 " pdb=" N PRO A 163 " pdb=" CA PRO A 163 " ideal model delta harmonic sigma weight residual -180.00 -123.95 -56.05 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA TYR D 140 " pdb=" C TYR D 140 " pdb=" N PRO D 141 " pdb=" CA PRO D 141 " ideal model delta harmonic sigma weight residual 0.00 32.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA ASN B 152 " pdb=" C ASN B 152 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 6062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1041 0.041 - 0.081: 362 0.081 - 0.122: 116 0.122 - 0.162: 21 0.162 - 0.203: 5 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA PRO D 141 " pdb=" N PRO D 141 " pdb=" C PRO D 141 " pdb=" CB PRO D 141 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO A 163 " pdb=" N PRO A 163 " pdb=" C PRO A 163 " pdb=" CB PRO A 163 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1542 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 162 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 163 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 112 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 113 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 140 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 141 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 740 2.74 - 3.28: 9048 3.28 - 3.82: 15202 3.82 - 4.36: 18990 4.36 - 4.90: 33934 Nonbonded interactions: 77914 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" O LEU H 116 " model vdw 2.195 3.040 nonbonded pdb=" O TYR D 192 " pdb=" OG SER D 208 " model vdw 2.220 3.040 nonbonded pdb=" NH1 ARG B 108 " pdb=" O ASP B 170 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR A 205 " pdb=" OE1 GLN A 206 " model vdw 2.246 3.040 nonbonded pdb=" O SER C 192 " pdb=" OH TYR C 198 " model vdw 2.263 3.040 ... (remaining 77909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.005 0.062 10142 Z= 0.335 Angle : 0.877 11.798 13794 Z= 0.514 Chirality : 0.047 0.203 1545 Planarity : 0.007 0.113 1765 Dihedral : 12.808 85.402 3659 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.86 (0.23), residues: 1276 helix: -3.28 (0.48), residues: 61 sheet: -0.57 (0.22), residues: 543 loop : -1.58 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 47 HIS 0.006 0.001 HIS A 214 PHE 0.018 0.002 PHE H 67 TYR 0.025 0.002 TYR M 495 ARG 0.010 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.188 Fit side-chains REVERT: B 145 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7774 (ttpt) REVERT: B 169 LYS cc_start: 0.7414 (ttpt) cc_final: 0.6864 (mmmt) REVERT: B 188 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6804 (ttmt) REVERT: B 190 LYS cc_start: 0.6283 (tptt) cc_final: 0.6062 (tptp) REVERT: C 203 ASN cc_start: 0.7070 (t0) cc_final: 0.6834 (t0) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 1.4231 time to fit residues: 272.8089 Evaluate side-chains 135 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 389 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN C 201 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN L 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10142 Z= 0.307 Angle : 0.704 9.996 13794 Z= 0.367 Chirality : 0.047 0.217 1545 Planarity : 0.007 0.110 1765 Dihedral : 5.945 55.861 1465 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.29 % Favored : 92.55 % Rotamer: Outliers : 2.45 % Allowed : 9.45 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.65 (0.23), residues: 1276 helix: -3.20 (0.50), residues: 54 sheet: -0.39 (0.23), residues: 540 loop : -1.49 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 47 HIS 0.007 0.002 HIS A 214 PHE 0.016 0.002 PHE M 374 TYR 0.020 0.002 TYR D 140 ARG 0.005 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.954 Fit side-chains REVERT: A 119 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: B 169 LYS cc_start: 0.7451 (ttpt) cc_final: 0.6881 (mmmt) REVERT: B 188 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6762 (ttmt) REVERT: B 195 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: C 109 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: D 27 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: L 83 PHE cc_start: 0.7296 (t80) cc_final: 0.7089 (t80) REVERT: M 339 ASP cc_start: 0.7679 (m-30) cc_final: 0.7456 (m-30) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 1.3587 time to fit residues: 240.2981 Evaluate side-chains 159 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 204 HIS L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10142 Z= 0.228 Angle : 0.640 8.173 13794 Z= 0.333 Chirality : 0.045 0.209 1545 Planarity : 0.006 0.106 1765 Dihedral : 5.673 55.101 1465 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 3.45 % Allowed : 11.45 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % 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: -1.48 (0.23), residues: 1276 helix: -3.16 (0.52), residues: 54 sheet: -0.23 (0.23), residues: 537 loop : -1.41 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.006 0.001 HIS A 214 PHE 0.014 0.001 PHE M 377 TYR 0.023 0.001 TYR D 140 ARG 0.011 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.191 Fit side-chains REVERT: A 119 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: B 169 LYS cc_start: 0.7440 (ttpt) cc_final: 0.6881 (mmmt) REVERT: B 188 LYS cc_start: 0.7093 (ttpt) cc_final: 0.6813 (ttmt) REVERT: C 109 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: H 115 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8602 (tt) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 1.2237 time to fit residues: 226.4499 Evaluate side-chains 162 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 211 ASN C 201 ASN H 39 GLN L 3 GLN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10142 Z= 0.175 Angle : 0.604 8.993 13794 Z= 0.312 Chirality : 0.044 0.219 1545 Planarity : 0.006 0.104 1765 Dihedral : 5.516 54.000 1465 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.43 % Favored : 93.41 % Rotamer: Outliers : 3.18 % Allowed : 13.82 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % 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: -1.26 (0.23), residues: 1276 helix: -2.95 (0.63), residues: 41 sheet: -0.08 (0.23), residues: 533 loop : -1.31 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.004 0.001 HIS A 214 PHE 0.013 0.001 PHE D 139 TYR 0.023 0.001 TYR D 140 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.143 Fit side-chains REVERT: A 119 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: B 145 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7410 (ttpt) REVERT: B 169 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6868 (mmmt) REVERT: B 188 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6745 (ttmt) REVERT: D 185 ASP cc_start: 0.5988 (t0) cc_final: 0.5767 (t0) REVERT: H 115 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8585 (tt) outliers start: 34 outliers final: 18 residues processed: 162 average time/residue: 1.2751 time to fit residues: 221.4058 Evaluate side-chains 148 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 213 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10142 Z= 0.295 Angle : 0.662 7.988 13794 Z= 0.344 Chirality : 0.046 0.212 1545 Planarity : 0.006 0.106 1765 Dihedral : 5.710 54.146 1463 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.53 % Favored : 92.31 % Rotamer: Outliers : 3.91 % Allowed : 14.18 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.08 % 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: -1.41 (0.23), residues: 1276 helix: -3.30 (0.50), residues: 54 sheet: -0.11 (0.23), residues: 539 loop : -1.42 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 PHE 0.023 0.002 PHE M 377 TYR 0.017 0.002 TYR C 33 ARG 0.012 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.190 Fit side-chains REVERT: A 119 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: B 126 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7566 (pttp) REVERT: B 145 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7441 (ttpt) REVERT: B 169 LYS cc_start: 0.7470 (ttpt) cc_final: 0.6901 (mmmt) REVERT: B 188 LYS cc_start: 0.7025 (ttpt) cc_final: 0.6714 (ttmt) REVERT: B 195 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7527 (tm-30) outliers start: 42 outliers final: 29 residues processed: 166 average time/residue: 1.2931 time to fit residues: 230.8372 Evaluate side-chains 155 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 73 ASN D 199 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10142 Z= 0.171 Angle : 0.609 9.278 13794 Z= 0.313 Chirality : 0.044 0.198 1545 Planarity : 0.006 0.102 1765 Dihedral : 5.486 53.360 1463 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.04 % Favored : 93.80 % Rotamer: Outliers : 3.36 % Allowed : 15.64 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % 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: -1.16 (0.23), residues: 1276 helix: -3.10 (0.61), residues: 41 sheet: 0.04 (0.23), residues: 536 loop : -1.28 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS B 189 PHE 0.014 0.001 PHE D 139 TYR 0.014 0.001 TYR D 140 ARG 0.011 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.160 Fit side-chains REVERT: A 119 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: B 145 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7504 (ttpt) REVERT: B 169 LYS cc_start: 0.7415 (ttpt) cc_final: 0.6861 (mmmt) REVERT: B 188 LYS cc_start: 0.7010 (ttpt) cc_final: 0.6717 (ttmt) REVERT: B 195 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: D 140 TYR cc_start: 0.7394 (t80) cc_final: 0.6983 (t80) REVERT: H 115 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8609 (tt) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 1.2385 time to fit residues: 221.5461 Evaluate side-chains 150 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 0.0020 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10142 Z= 0.205 Angle : 0.617 7.475 13794 Z= 0.318 Chirality : 0.045 0.212 1545 Planarity : 0.006 0.103 1765 Dihedral : 5.443 52.997 1463 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 3.73 % Allowed : 16.82 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.11 (0.23), residues: 1276 helix: -3.12 (0.60), residues: 41 sheet: 0.06 (0.23), residues: 537 loop : -1.23 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.004 0.001 HIS A 214 PHE 0.015 0.001 PHE M 377 TYR 0.016 0.001 TYR D 140 ARG 0.010 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.233 Fit side-chains REVERT: A 70 MET cc_start: 0.7919 (mtt) cc_final: 0.7635 (mtt) REVERT: A 119 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: B 145 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7463 (ttpt) REVERT: B 169 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6882 (mmmt) REVERT: B 188 LYS cc_start: 0.6937 (ttpt) cc_final: 0.6710 (ttmt) REVERT: B 195 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: D 140 TYR cc_start: 0.7363 (t80) cc_final: 0.7036 (t80) REVERT: H 115 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8609 (tt) outliers start: 40 outliers final: 29 residues processed: 165 average time/residue: 1.2154 time to fit residues: 215.7886 Evaluate side-chains 157 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10142 Z= 0.277 Angle : 0.657 7.276 13794 Z= 0.340 Chirality : 0.046 0.207 1545 Planarity : 0.006 0.104 1765 Dihedral : 5.616 53.179 1463 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 3.91 % Allowed : 16.18 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % 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: -1.25 (0.23), residues: 1276 helix: -3.27 (0.50), residues: 54 sheet: 0.04 (0.23), residues: 542 loop : -1.36 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 PHE 0.020 0.002 PHE M 377 TYR 0.016 0.002 TYR C 33 ARG 0.012 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.184 Fit side-chains REVERT: A 70 MET cc_start: 0.7944 (mtt) cc_final: 0.7708 (mtt) REVERT: A 119 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: B 169 LYS cc_start: 0.7448 (ttpt) cc_final: 0.6894 (mmmt) REVERT: B 188 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6741 (ttmt) REVERT: B 195 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: D 140 TYR cc_start: 0.7540 (t80) cc_final: 0.7052 (t80) REVERT: H 115 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8648 (tt) outliers start: 42 outliers final: 37 residues processed: 156 average time/residue: 1.0998 time to fit residues: 186.2198 Evaluate side-chains 162 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.0070 chunk 111 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 73 ASN C 201 ASN D 138 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10142 Z= 0.168 Angle : 0.607 6.937 13794 Z= 0.313 Chirality : 0.044 0.218 1545 Planarity : 0.006 0.100 1765 Dihedral : 5.359 52.544 1463 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 3.18 % Allowed : 17.55 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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 (0.23), residues: 1276 helix: -3.14 (0.60), residues: 41 sheet: 0.20 (0.23), residues: 536 loop : -1.23 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS A 214 PHE 0.013 0.001 PHE D 139 TYR 0.017 0.001 TYR D 140 ARG 0.014 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.124 Fit side-chains REVERT: A 70 MET cc_start: 0.7882 (mtt) cc_final: 0.7623 (mtt) REVERT: A 73 ASP cc_start: 0.8073 (t70) cc_final: 0.7688 (t70) REVERT: A 119 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: B 169 LYS cc_start: 0.7412 (ttpt) cc_final: 0.6861 (mmmt) REVERT: B 188 LYS cc_start: 0.6906 (ttpt) cc_final: 0.6639 (ttmt) REVERT: D 140 TYR cc_start: 0.7243 (t80) cc_final: 0.6984 (t80) REVERT: H 115 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8589 (tt) outliers start: 34 outliers final: 29 residues processed: 158 average time/residue: 1.2553 time to fit residues: 213.1150 Evaluate side-chains 159 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 90 GLN D 138 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10142 Z= 0.274 Angle : 0.661 7.937 13794 Z= 0.340 Chirality : 0.046 0.207 1545 Planarity : 0.006 0.104 1765 Dihedral : 5.554 52.690 1463 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 3.36 % Allowed : 17.55 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.16 (0.23), residues: 1276 helix: -3.25 (0.50), residues: 54 sheet: 0.13 (0.23), residues: 542 loop : -1.32 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS A 214 PHE 0.017 0.002 PHE M 377 TYR 0.016 0.002 TYR C 33 ARG 0.013 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.106 Fit side-chains REVERT: A 70 MET cc_start: 0.7927 (mtt) cc_final: 0.7697 (mtt) REVERT: A 119 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 169 LYS cc_start: 0.7478 (ttpt) cc_final: 0.6904 (mmmt) REVERT: B 188 LYS cc_start: 0.6853 (ttpt) cc_final: 0.6629 (ttmt) REVERT: C 160 SER cc_start: 0.8552 (m) cc_final: 0.7988 (p) REVERT: D 140 TYR cc_start: 0.7380 (t80) cc_final: 0.7092 (t80) REVERT: H 115 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8655 (tt) outliers start: 36 outliers final: 29 residues processed: 150 average time/residue: 1.1360 time to fit residues: 185.9207 Evaluate side-chains 154 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.0030 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 90 GLN D 138 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122455 restraints weight = 16995.436| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.46 r_work: 0.3428 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10142 Z= 0.161 Angle : 0.602 6.906 13794 Z= 0.310 Chirality : 0.044 0.216 1545 Planarity : 0.006 0.099 1765 Dihedral : 5.300 52.068 1463 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.73 % Rotamer: Outliers : 3.00 % Allowed : 17.91 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.98 (0.24), residues: 1276 helix: -3.06 (0.58), residues: 45 sheet: 0.21 (0.23), residues: 543 loop : -1.21 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS A 214 PHE 0.013 0.001 PHE D 139 TYR 0.018 0.001 TYR D 140 ARG 0.014 0.001 ARG B 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4266.92 seconds wall clock time: 77 minutes 3.01 seconds (4623.01 seconds total)