Starting phenix.real_space_refine on Fri Jan 17 03:48:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgm_38328/01_2025/8xgm_38328.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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 66 5.16 5 C 6615 2.51 5 N 1756 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10319 Number of models: 1 Model: "" Number of chains: 7 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2539 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2589 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1850 Classifications: {'peptide': 233} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 230} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "D" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1117 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.21, per 1000 atoms: 0.60 Number of scatterers: 10319 At special positions: 0 Unit cell: (99.45, 104.55, 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 66 16.00 O 1882 8.00 N 1756 7.00 C 6615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 97 " distance=2.02 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 115 " 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 33.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.892A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 65 removed outlier: 3.864A pdb=" N TRP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Proline residue: A 54 - end of helix removed outlier: 3.615A pdb=" N PHE A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.541A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.930A pdb=" N TYR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.839A pdb=" N CYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.917A pdb=" N ARG A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 170 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 215 through 237 removed outlier: 3.957A pdb=" N ILE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 removed outlier: 3.629A pdb=" N VAL A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 4.760A pdb=" N PHE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 285 through 305 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.534A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 241 through 254 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.200A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.824A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.855A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'D' and resid 4 through 19 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.613A pdb=" N ARG D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.755A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.364A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.505A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.826A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.974A pdb=" N GLU A 25 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG D 93 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 92 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE D 45 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP D 37 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 47 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA D 35 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU D 49 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN D 53 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU D 29 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.217A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.680A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.880A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.234A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.582A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.873A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.708A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 6.164A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1332 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: 3.08 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1662 1.32 - 1.45: 2984 1.45 - 1.57: 5827 1.57 - 1.70: 1 1.70 - 1.83: 92 Bond restraints: 10566 Sorted by residual: bond pdb=" CA ARG C 21 " pdb=" C ARG C 21 " ideal model delta sigma weight residual 1.524 1.450 0.073 1.27e-02 6.20e+03 3.34e+01 bond pdb=" CA ALA C 338 " pdb=" CB ALA C 338 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.59e-02 3.96e+03 2.23e+01 bond pdb=" N ALA C 338 " pdb=" CA ALA C 338 " ideal model delta sigma weight residual 1.459 1.404 0.055 1.23e-02 6.61e+03 1.99e+01 bond pdb=" C VAL C 335 " pdb=" O VAL C 335 " ideal model delta sigma weight residual 1.237 1.191 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" CA VAL C 335 " pdb=" CB VAL C 335 " ideal model delta sigma weight residual 1.540 1.492 0.048 1.25e-02 6.40e+03 1.49e+01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 13994 2.03 - 4.07: 274 4.07 - 6.10: 42 6.10 - 8.13: 13 8.13 - 10.17: 2 Bond angle restraints: 14325 Sorted by residual: angle pdb=" N GLU S 234 " pdb=" CA GLU S 234 " pdb=" C GLU S 234 " ideal model delta sigma weight residual 109.95 100.61 9.34 1.59e+00 3.96e-01 3.45e+01 angle pdb=" N LEU S 233 " pdb=" CA LEU S 233 " pdb=" C LEU S 233 " ideal model delta sigma weight residual 111.11 104.85 6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" N LYS D 19 " pdb=" CA LYS D 19 " pdb=" C LYS D 19 " ideal model delta sigma weight residual 113.02 107.45 5.57 1.20e+00 6.94e-01 2.16e+01 angle pdb=" N VAL C 335 " pdb=" CA VAL C 335 " pdb=" C VAL C 335 " ideal model delta sigma weight residual 110.62 105.97 4.65 1.02e+00 9.61e-01 2.07e+01 angle pdb=" C ARG C 21 " pdb=" CA ARG C 21 " pdb=" CB ARG C 21 " ideal model delta sigma weight residual 110.88 104.41 6.47 1.57e+00 4.06e-01 1.70e+01 ... (remaining 14320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 5673 24.45 - 48.89: 542 48.89 - 73.34: 60 73.34 - 97.79: 7 97.79 - 122.24: 3 Dihedral angle restraints: 6285 sinusoidal: 2502 harmonic: 3783 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -165.92 79.92 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" C10 CLR A 401 " pdb=" C1 CLR A 401 " pdb=" C2 CLR A 401 " pdb=" C3 CLR A 401 " ideal model delta sinusoidal sigma weight residual -56.83 65.41 -122.24 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1449 0.075 - 0.150: 148 0.150 - 0.225: 6 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" C13 CLR A 401 " pdb=" C12 CLR A 401 " pdb=" C14 CLR A 401 " pdb=" C17 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.56 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C14 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C15 CLR A 401 " pdb=" C8 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU C 348 " pdb=" N LEU C 348 " pdb=" C LEU C 348 " pdb=" CB LEU C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1602 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 18 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C HIS D 18 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS D 18 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS D 19 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 96 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C HIS D 96 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS D 96 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS D 97 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 281 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO C 282 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 282 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 282 " 0.032 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 222 2.67 - 3.23: 9663 3.23 - 3.78: 15563 3.78 - 4.34: 20512 4.34 - 4.90: 35126 Nonbonded interactions: 81086 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.112 3.040 nonbonded pdb=" NZ LYS S 244 " pdb=" OE2 GLU S 246 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLN A 118 " pdb=" OG SER D 137 " model vdw 2.201 3.040 nonbonded pdb=" NZ LYS D 83 " pdb=" O ALA D 121 " model vdw 2.230 3.120 nonbonded pdb=" O HIS A 141 " pdb=" OG SER A 145 " model vdw 2.247 3.040 ... (remaining 81081 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=1.00 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: 1.560 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.004 0.088 10566 Z= 0.293 Angle : 0.692 10.168 14325 Z= 0.387 Chirality : 0.046 0.375 1605 Planarity : 0.005 0.058 1802 Dihedral : 17.553 122.237 3823 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.36 % Allowed : 30.26 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1285 helix: 1.02 (0.26), residues: 413 sheet: -0.37 (0.26), residues: 346 loop : -1.68 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 36 HIS 0.008 0.001 HIS D 18 PHE 0.013 0.001 PHE C 189 TYR 0.028 0.002 TYR S 235 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: S 38 ARG cc_start: 0.5373 (ttp-170) cc_final: 0.4563 (ttm-80) REVERT: S 60 TYR cc_start: 0.4605 (m-80) cc_final: 0.3784 (m-80) REVERT: S 98 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6823 (ptm-80) REVERT: S 141 THR cc_start: 0.5403 (m) cc_final: 0.5072 (p) REVERT: S 230 MET cc_start: 0.7161 (tmm) cc_final: 0.6921 (tmm) REVERT: C 251 ASP cc_start: 0.8384 (t0) cc_final: 0.8181 (t0) REVERT: C 252 SER cc_start: 0.8148 (t) cc_final: 0.7734 (p) outliers start: 4 outliers final: 2 residues processed: 151 average time/residue: 0.2652 time to fit residues: 56.0975 Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 348 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 38 optimal weight: 0.0040 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 chunk 115 optimal weight: 6.9990 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 194 ASN A 192 GLN B 259 GLN D 54 GLN D 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125330 restraints weight = 13738.442| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.23 r_work: 0.3359 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10566 Z= 0.145 Angle : 0.563 8.832 14325 Z= 0.293 Chirality : 0.042 0.146 1605 Planarity : 0.004 0.054 1802 Dihedral : 5.157 44.434 1471 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.49 % Allowed : 27.66 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1285 helix: 1.64 (0.26), residues: 414 sheet: -0.11 (0.28), residues: 336 loop : -1.47 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 75 HIS 0.006 0.001 HIS D 20 PHE 0.015 0.001 PHE A 105 TYR 0.026 0.001 TYR S 235 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.145 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: S 38 ARG cc_start: 0.5411 (ttp-170) cc_final: 0.4522 (ttm-80) REVERT: S 60 TYR cc_start: 0.4522 (m-80) cc_final: 0.3798 (m-80) REVERT: S 141 THR cc_start: 0.5649 (m) cc_final: 0.5249 (p) REVERT: S 233 LEU cc_start: 0.7088 (tm) cc_final: 0.6783 (tm) REVERT: B 27 ASP cc_start: 0.7439 (t0) cc_final: 0.7214 (t0) REVERT: B 292 PHE cc_start: 0.8453 (m-80) cc_final: 0.8033 (m-80) REVERT: C 26 ASP cc_start: 0.7408 (t0) cc_final: 0.7208 (t0) REVERT: C 227 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7901 (pp) REVERT: C 251 ASP cc_start: 0.8202 (t0) cc_final: 0.7955 (t0) REVERT: C 252 SER cc_start: 0.8347 (t) cc_final: 0.7818 (p) REVERT: C 269 ASN cc_start: 0.8561 (m-40) cc_final: 0.8307 (m-40) REVERT: C 305 CYS cc_start: 0.7821 (t) cc_final: 0.7397 (t) REVERT: C 309 ASP cc_start: 0.7816 (m-30) cc_final: 0.7514 (m-30) REVERT: C 328 ASP cc_start: 0.7107 (m-30) cc_final: 0.6887 (m-30) REVERT: G 32 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7896 (ttpp) REVERT: G 36 ASP cc_start: 0.7765 (m-30) cc_final: 0.7513 (m-30) REVERT: D 88 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7185 (t70) REVERT: D 124 ASP cc_start: 0.7747 (t0) cc_final: 0.7488 (t0) REVERT: D 133 GLN cc_start: 0.7597 (mt0) cc_final: 0.7355 (mt0) outliers start: 39 outliers final: 17 residues processed: 195 average time/residue: 0.2391 time to fit residues: 66.0499 Evaluate side-chains 175 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 86 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 192 GLN B 220 GLN C 241 ASN D 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.182526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123768 restraints weight = 14106.874| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.31 r_work: 0.3373 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10566 Z= 0.153 Angle : 0.548 7.811 14325 Z= 0.285 Chirality : 0.041 0.143 1605 Planarity : 0.004 0.053 1802 Dihedral : 4.494 48.814 1467 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.31 % Allowed : 27.66 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1285 helix: 1.77 (0.26), residues: 415 sheet: 0.06 (0.28), residues: 336 loop : -1.47 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 75 HIS 0.006 0.001 HIS D 20 PHE 0.012 0.001 PHE C 189 TYR 0.026 0.001 TYR S 235 ARG 0.003 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.072 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: S 60 TYR cc_start: 0.5020 (m-80) cc_final: 0.4210 (m-80) REVERT: S 233 LEU cc_start: 0.7096 (tm) cc_final: 0.6874 (tm) REVERT: A 192 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: B 27 ASP cc_start: 0.7176 (t0) cc_final: 0.6898 (t0) REVERT: B 292 PHE cc_start: 0.8482 (m-80) cc_final: 0.8026 (m-80) REVERT: C 26 ASP cc_start: 0.7471 (t0) cc_final: 0.7188 (t0) REVERT: C 227 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7971 (pp) REVERT: C 251 ASP cc_start: 0.8190 (t0) cc_final: 0.7945 (t0) REVERT: C 252 SER cc_start: 0.8401 (t) cc_final: 0.7872 (p) REVERT: C 309 ASP cc_start: 0.7834 (m-30) cc_final: 0.7498 (m-30) REVERT: G 32 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7878 (ttpp) REVERT: G 36 ASP cc_start: 0.7700 (m-30) cc_final: 0.7439 (m-30) REVERT: D 133 GLN cc_start: 0.7536 (mt0) cc_final: 0.7283 (mt0) outliers start: 37 outliers final: 26 residues processed: 188 average time/residue: 0.2234 time to fit residues: 59.6352 Evaluate side-chains 185 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain D residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.182520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124608 restraints weight = 13762.348| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.21 r_work: 0.3375 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10566 Z= 0.164 Angle : 0.540 8.652 14325 Z= 0.280 Chirality : 0.041 0.146 1605 Planarity : 0.004 0.046 1802 Dihedral : 4.518 52.089 1467 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.66 % Allowed : 27.84 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1285 helix: 1.83 (0.26), residues: 414 sheet: 0.10 (0.28), residues: 337 loop : -1.41 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.005 0.001 HIS D 20 PHE 0.012 0.001 PHE C 189 TYR 0.025 0.001 TYR S 235 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 1.144 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 18 ARG cc_start: 0.5921 (mmm-85) cc_final: 0.5621 (mmm-85) REVERT: S 60 TYR cc_start: 0.5563 (m-80) cc_final: 0.4674 (m-80) REVERT: S 141 THR cc_start: 0.5654 (m) cc_final: 0.5280 (p) REVERT: S 171 ASN cc_start: 0.6894 (m-40) cc_final: 0.6478 (m-40) REVERT: B 27 ASP cc_start: 0.7255 (t0) cc_final: 0.6951 (t0) REVERT: B 198 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 292 PHE cc_start: 0.8538 (m-80) cc_final: 0.8022 (m-80) REVERT: C 26 ASP cc_start: 0.7442 (t0) cc_final: 0.7114 (t0) REVERT: C 227 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8015 (pp) REVERT: C 252 SER cc_start: 0.8440 (t) cc_final: 0.7929 (p) REVERT: C 309 ASP cc_start: 0.7688 (m-30) cc_final: 0.7336 (m-30) REVERT: G 32 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7927 (ttpp) REVERT: G 36 ASP cc_start: 0.7721 (m-30) cc_final: 0.7446 (m-30) REVERT: D 45 PHE cc_start: 0.7080 (t80) cc_final: 0.6864 (t80) REVERT: D 79 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6361 (tp) REVERT: D 133 GLN cc_start: 0.7564 (mt0) cc_final: 0.7301 (mt0) outliers start: 52 outliers final: 32 residues processed: 203 average time/residue: 0.2122 time to fit residues: 62.3618 Evaluate side-chains 199 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 112 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117426 restraints weight = 13862.992| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.21 r_work: 0.3272 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10566 Z= 0.302 Angle : 0.616 8.397 14325 Z= 0.325 Chirality : 0.044 0.158 1605 Planarity : 0.004 0.046 1802 Dihedral : 4.844 50.653 1467 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.74 % Allowed : 27.66 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1285 helix: 1.61 (0.26), residues: 415 sheet: -0.17 (0.28), residues: 344 loop : -1.37 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS D 20 PHE 0.015 0.002 PHE B 241 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 1.155 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 18 ARG cc_start: 0.5994 (mmm-85) cc_final: 0.5778 (mmm-85) REVERT: S 60 TYR cc_start: 0.6085 (m-80) cc_final: 0.5275 (m-80) REVERT: S 171 ASN cc_start: 0.7045 (m-40) cc_final: 0.6667 (m-40) REVERT: S 180 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6753 (tmt-80) REVERT: A 68 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8187 (ttpp) REVERT: B 27 ASP cc_start: 0.7604 (t0) cc_final: 0.7329 (t0) REVERT: B 292 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: C 22 ASN cc_start: 0.7673 (t0) cc_final: 0.7382 (t0) REVERT: C 26 ASP cc_start: 0.7588 (t0) cc_final: 0.7228 (t0) REVERT: C 227 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 306 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7591 (tp40) REVERT: C 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7412 (m-30) REVERT: D 45 PHE cc_start: 0.7248 (t80) cc_final: 0.6855 (t80) REVERT: D 79 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6426 (tp) REVERT: D 83 LYS cc_start: 0.6697 (ptmm) cc_final: 0.6478 (pttm) outliers start: 53 outliers final: 34 residues processed: 205 average time/residue: 0.2045 time to fit residues: 60.8232 Evaluate side-chains 197 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 192 GLN D 11 GLN D 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117832 restraints weight = 14140.453| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.13 r_work: 0.3341 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10566 Z= 0.204 Angle : 0.570 7.685 14325 Z= 0.299 Chirality : 0.042 0.154 1605 Planarity : 0.004 0.054 1802 Dihedral : 4.764 51.627 1467 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.01 % Allowed : 29.10 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1285 helix: 1.70 (0.26), residues: 413 sheet: -0.08 (0.29), residues: 321 loop : -1.35 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 111 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE C 189 TYR 0.024 0.001 TYR S 235 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 1.099 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 60 TYR cc_start: 0.6022 (m-80) cc_final: 0.5230 (m-80) REVERT: S 83 MET cc_start: 0.5749 (mtp) cc_final: 0.5197 (ttm) REVERT: S 171 ASN cc_start: 0.7177 (m-40) cc_final: 0.6839 (m-40) REVERT: A 192 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: A 282 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.7994 (mtp) REVERT: B 27 ASP cc_start: 0.7600 (t0) cc_final: 0.7315 (t0) REVERT: B 198 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8329 (mt) REVERT: B 292 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: C 22 ASN cc_start: 0.7782 (t0) cc_final: 0.7499 (t0) REVERT: C 26 ASP cc_start: 0.7696 (t0) cc_final: 0.7315 (t0) REVERT: C 227 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8096 (pp) REVERT: C 309 ASP cc_start: 0.7770 (m-30) cc_final: 0.7399 (m-30) REVERT: G 32 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7888 (ttpp) REVERT: G 36 ASP cc_start: 0.7963 (m-30) cc_final: 0.7595 (m-30) REVERT: D 11 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8617 (pp30) REVERT: D 45 PHE cc_start: 0.7472 (t80) cc_final: 0.7272 (t80) REVERT: D 79 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6476 (tp) REVERT: D 83 LYS cc_start: 0.6835 (ptmm) cc_final: 0.6629 (pttm) outliers start: 56 outliers final: 36 residues processed: 203 average time/residue: 0.2127 time to fit residues: 63.0918 Evaluate side-chains 204 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 192 GLN D 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116679 restraints weight = 14299.309| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.14 r_work: 0.3325 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.003 0.035 10566 Z= 0.228 Angle : 0.578 9.341 14325 Z= 0.302 Chirality : 0.043 0.155 1605 Planarity : 0.004 0.053 1802 Dihedral : 4.783 51.464 1467 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.19 % Allowed : 29.19 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1285 helix: 1.63 (0.26), residues: 414 sheet: -0.15 (0.28), residues: 331 loop : -1.34 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 111 HIS 0.007 0.001 HIS S 167 PHE 0.014 0.001 PHE C 189 TYR 0.025 0.001 TYR S 235 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.235 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 60 TYR cc_start: 0.6028 (m-80) cc_final: 0.5168 (m-80) REVERT: S 171 ASN cc_start: 0.7241 (m-40) cc_final: 0.6927 (m-40) REVERT: A 68 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8266 (ttpp) REVERT: A 192 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: A 282 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: B 27 ASP cc_start: 0.7624 (t0) cc_final: 0.7365 (t0) REVERT: B 198 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8366 (mt) REVERT: B 292 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: C 22 ASN cc_start: 0.7786 (t0) cc_final: 0.7501 (t0) REVERT: C 26 ASP cc_start: 0.7713 (t0) cc_final: 0.7334 (t0) REVERT: C 227 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8110 (pp) REVERT: C 306 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7407 (tp40) REVERT: C 309 ASP cc_start: 0.7764 (m-30) cc_final: 0.7479 (m-30) REVERT: G 32 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7896 (ttpp) REVERT: G 36 ASP cc_start: 0.7964 (m-30) cc_final: 0.7590 (m-30) REVERT: D 79 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6855 (tp) REVERT: D 81 CYS cc_start: 0.6323 (t) cc_final: 0.5833 (t) REVERT: D 83 LYS cc_start: 0.6997 (ptmm) cc_final: 0.6783 (pttm) outliers start: 58 outliers final: 40 residues processed: 201 average time/residue: 0.2133 time to fit residues: 61.5611 Evaluate side-chains 204 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 340 ASN D 11 GLN D 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113680 restraints weight = 14064.881| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.19 r_work: 0.3213 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10566 Z= 0.417 Angle : 0.674 9.324 14325 Z= 0.357 Chirality : 0.047 0.173 1605 Planarity : 0.005 0.056 1802 Dihedral : 5.210 50.808 1467 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.28 % Allowed : 29.72 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1285 helix: 1.33 (0.26), residues: 413 sheet: -0.44 (0.27), residues: 334 loop : -1.43 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 111 HIS 0.009 0.002 HIS S 167 PHE 0.045 0.002 PHE D 45 TYR 0.025 0.002 TYR S 235 ARG 0.005 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: S 60 TYR cc_start: 0.6179 (m-80) cc_final: 0.5324 (m-80) REVERT: S 141 THR cc_start: 0.5531 (m) cc_final: 0.5166 (p) REVERT: S 171 ASN cc_start: 0.7169 (m-40) cc_final: 0.6901 (m-40) REVERT: A 268 TRP cc_start: 0.8361 (t60) cc_final: 0.8015 (t60) REVERT: B 292 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: C 22 ASN cc_start: 0.7685 (t0) cc_final: 0.7449 (t0) REVERT: C 26 ASP cc_start: 0.7600 (t0) cc_final: 0.7238 (t0) REVERT: C 227 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (pp) REVERT: C 305 CYS cc_start: 0.7961 (t) cc_final: 0.7409 (t) REVERT: C 306 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7588 (tp40) REVERT: C 309 ASP cc_start: 0.7688 (m-30) cc_final: 0.7340 (m-30) REVERT: G 32 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7841 (ttpp) REVERT: G 36 ASP cc_start: 0.8033 (m-30) cc_final: 0.7645 (m-30) outliers start: 59 outliers final: 39 residues processed: 204 average time/residue: 0.2037 time to fit residues: 60.3258 Evaluate side-chains 188 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.0670 chunk 116 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN D 11 GLN D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118507 restraints weight = 14117.711| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.12 r_work: 0.3347 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10566 Z= 0.159 Angle : 0.572 8.680 14325 Z= 0.298 Chirality : 0.042 0.152 1605 Planarity : 0.004 0.061 1802 Dihedral : 4.899 50.534 1467 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.85 % Allowed : 31.07 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1285 helix: 1.67 (0.26), residues: 412 sheet: -0.17 (0.28), residues: 318 loop : -1.34 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 75 HIS 0.009 0.001 HIS D 20 PHE 0.037 0.001 PHE D 45 TYR 0.024 0.001 TYR S 235 ARG 0.007 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.074 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 60 TYR cc_start: 0.6034 (m-80) cc_final: 0.5263 (m-80) REVERT: S 171 ASN cc_start: 0.7160 (m-40) cc_final: 0.6914 (m-40) REVERT: A 68 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8254 (ttpp) REVERT: A 282 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7938 (mtp) REVERT: B 27 ASP cc_start: 0.7606 (t0) cc_final: 0.7267 (t0) REVERT: C 21 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6880 (mtm110) REVERT: C 22 ASN cc_start: 0.7727 (t0) cc_final: 0.7421 (t0) REVERT: C 26 ASP cc_start: 0.7710 (t0) cc_final: 0.7341 (t0) REVERT: C 309 ASP cc_start: 0.7789 (m-30) cc_final: 0.7380 (m-30) REVERT: G 32 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7997 (ttpp) REVERT: D 11 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8580 (pp30) REVERT: D 79 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6997 (tp) outliers start: 43 outliers final: 32 residues processed: 195 average time/residue: 0.2190 time to fit residues: 60.9823 Evaluate side-chains 194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.172682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115243 restraints weight = 14182.149| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.10 r_work: 0.3303 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10566 Z= 0.284 Angle : 0.610 8.893 14325 Z= 0.319 Chirality : 0.044 0.160 1605 Planarity : 0.004 0.056 1802 Dihedral : 4.966 49.959 1467 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.58 % Allowed : 31.78 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1285 helix: 1.66 (0.26), residues: 413 sheet: -0.30 (0.28), residues: 326 loop : -1.34 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.008 0.001 HIS D 18 PHE 0.037 0.002 PHE D 45 TYR 0.026 0.002 TYR S 235 ARG 0.006 0.000 ARG C 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.225 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 60 TYR cc_start: 0.6212 (m-80) cc_final: 0.5427 (m-80) REVERT: S 171 ASN cc_start: 0.7198 (m-40) cc_final: 0.6949 (m-40) REVERT: A 268 TRP cc_start: 0.8330 (t60) cc_final: 0.8014 (t60) REVERT: B 27 ASP cc_start: 0.7695 (t0) cc_final: 0.7304 (t0) REVERT: B 292 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: C 21 ARG cc_start: 0.7338 (ttp80) cc_final: 0.6866 (mtm110) REVERT: C 22 ASN cc_start: 0.7788 (t0) cc_final: 0.7455 (t0) REVERT: C 26 ASP cc_start: 0.7721 (t0) cc_final: 0.7352 (t0) REVERT: C 305 CYS cc_start: 0.8114 (t) cc_final: 0.7488 (t) REVERT: C 309 ASP cc_start: 0.7857 (m-30) cc_final: 0.7350 (m-30) REVERT: G 32 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7982 (ttpp) outliers start: 40 outliers final: 36 residues processed: 185 average time/residue: 0.2118 time to fit residues: 56.2604 Evaluate side-chains 192 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 77 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115958 restraints weight = 14045.749| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.09 r_work: 0.3313 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10566 Z= 0.246 Angle : 0.600 8.751 14325 Z= 0.313 Chirality : 0.043 0.161 1605 Planarity : 0.004 0.056 1802 Dihedral : 4.971 49.959 1467 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.76 % Allowed : 31.60 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1285 helix: 1.68 (0.26), residues: 413 sheet: -0.23 (0.28), residues: 317 loop : -1.31 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.007 0.001 HIS D 18 PHE 0.035 0.001 PHE D 45 TYR 0.024 0.002 TYR S 235 ARG 0.006 0.000 ARG C 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5469.66 seconds wall clock time: 98 minutes 49.98 seconds (5929.98 seconds total)