Starting phenix.real_space_refine on Wed Sep 17 18:10:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgm_38328/09_2025/8xgm_38328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgm_38328/09_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_38328/09_2025/8xgm_38328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgm_38328/09_2025/8xgm_38328.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgm_38328/09_2025/8xgm_38328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgm_38328/09_2025/8xgm_38328.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 3, 'GLU:plan': 1} 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: 2.48, per 1000 atoms: 0.24 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: 0.97 Conformation dependent library (CDL) restraints added in 432.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.37 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: 1.72 Time building geometry restraints manager: 1.27 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: 2.210 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- 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 10572 Z= 0.249 Angle : 0.692 10.168 14337 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 : 10.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG C 208 TYR 0.028 0.002 TYR S 235 PHE 0.013 0.001 PHE C 189 TRP 0.021 0.001 TRP S 36 HIS 0.008 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00444 (10566) covalent geometry : angle 0.69192 (14325) SS BOND : bond 0.00542 ( 6) SS BOND : angle 1.10465 ( 12) hydrogen bonds : bond 0.12945 ( 459) hydrogen bonds : angle 6.19383 ( 1332) *********************** 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 : 0.431 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: 0.1178 time to fit residues: 24.4086 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 : 0.397 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 259 GLN D 11 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 = 0.4112 r_free = 0.4112 target = 0.179103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119750 restraints weight = 13984.074| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.26 r_work: 0.3328 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10572 Z= 0.132 Angle : 0.584 8.655 14337 Z= 0.305 Chirality : 0.042 0.150 1605 Planarity : 0.004 0.053 1802 Dihedral : 5.251 45.506 1471 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.12 % Allowed : 26.95 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.24), residues: 1285 helix: 1.57 (0.26), residues: 412 sheet: -0.18 (0.27), residues: 337 loop : -1.52 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.029 0.001 TYR S 235 PHE 0.013 0.001 PHE A 105 TRP 0.011 0.001 TRP A 75 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (10566) covalent geometry : angle 0.58314 (14325) SS BOND : bond 0.00357 ( 6) SS BOND : angle 0.96493 ( 12) hydrogen bonds : bond 0.04254 ( 459) hydrogen bonds : angle 4.77736 ( 1332) *********************** 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 210 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.455 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: 0.5391 (ttp-170) cc_final: 0.4546 (ttm-80) REVERT: S 60 TYR cc_start: 0.5124 (m-80) cc_final: 0.4279 (m-80) REVERT: S 141 THR cc_start: 0.5645 (m) cc_final: 0.5235 (p) REVERT: S 233 LEU cc_start: 0.7138 (tm) cc_final: 0.6835 (tm) REVERT: B 27 ASP cc_start: 0.7635 (t0) cc_final: 0.7434 (t0) REVERT: B 259 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 292 PHE cc_start: 0.8570 (m-80) cc_final: 0.8018 (m-80) REVERT: C 227 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7898 (pp) REVERT: C 251 ASP cc_start: 0.8272 (t0) cc_final: 0.8011 (t0) REVERT: C 252 SER cc_start: 0.8415 (t) cc_final: 0.7863 (p) REVERT: C 269 ASN cc_start: 0.8573 (m-40) cc_final: 0.8363 (m-40) REVERT: C 305 CYS cc_start: 0.7844 (t) cc_final: 0.7447 (t) REVERT: C 306 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7641 (tp40) REVERT: C 309 ASP cc_start: 0.7828 (m-30) cc_final: 0.7610 (m-30) REVERT: G 32 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7893 (ttpp) REVERT: G 36 ASP cc_start: 0.7867 (m-30) cc_final: 0.7624 (m-30) REVERT: D 79 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6302 (tp) REVERT: D 88 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7389 (t70) REVERT: D 124 ASP cc_start: 0.7753 (t0) cc_final: 0.7535 (t0) REVERT: D 126 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7440 (p-80) outliers start: 46 outliers final: 25 residues processed: 193 average time/residue: 0.1032 time to fit residues: 28.4205 Evaluate side-chains 186 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 ILE 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 128 THR 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 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN 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 C residue 306 GLN 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 Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 126 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 C 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120642 restraints weight = 14085.294| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.27 r_work: 0.3341 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10572 Z= 0.114 Angle : 0.560 8.333 14337 Z= 0.292 Chirality : 0.041 0.146 1605 Planarity : 0.004 0.051 1802 Dihedral : 4.642 48.786 1467 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.12 % Allowed : 27.66 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1285 helix: 1.66 (0.26), residues: 414 sheet: -0.08 (0.27), residues: 341 loop : -1.51 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.026 0.001 TYR S 235 PHE 0.013 0.001 PHE C 189 TRP 0.010 0.001 TRP A 75 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00250 (10566) covalent geometry : angle 0.55658 (14325) SS BOND : bond 0.00406 ( 6) SS BOND : angle 2.05189 ( 12) hydrogen bonds : bond 0.03881 ( 459) hydrogen bonds : angle 4.52505 ( 1332) *********************** 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 210 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.476 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: 0.5521 (m-80) cc_final: 0.4679 (m-80) REVERT: A 192 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: B 27 ASP cc_start: 0.7552 (t0) cc_final: 0.7315 (t0) REVERT: B 292 PHE cc_start: 0.8556 (m-80) cc_final: 0.8022 (m-80) REVERT: C 227 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7993 (pp) REVERT: C 251 ASP cc_start: 0.8258 (t0) cc_final: 0.7979 (t0) REVERT: C 252 SER cc_start: 0.8408 (t) cc_final: 0.7863 (p) REVERT: C 309 ASP cc_start: 0.7841 (m-30) cc_final: 0.7513 (m-30) REVERT: G 32 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7898 (ttpp) REVERT: G 36 ASP cc_start: 0.7773 (m-30) cc_final: 0.7520 (m-30) REVERT: D 79 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6363 (tp) REVERT: D 83 LYS cc_start: 0.6077 (ptmm) cc_final: 0.5854 (pttm) REVERT: D 124 ASP cc_start: 0.7899 (t0) cc_final: 0.7562 (t0) REVERT: D 126 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7431 (p-80) outliers start: 46 outliers final: 24 residues processed: 198 average time/residue: 0.1002 time to fit residues: 28.5593 Evaluate side-chains 192 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 180 GLU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 103 CYS 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 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 32 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 126 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.0170 chunk 106 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.175528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116404 restraints weight = 14004.871| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.22 r_work: 0.3256 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10572 Z= 0.213 Angle : 0.637 8.320 14337 Z= 0.334 Chirality : 0.045 0.169 1605 Planarity : 0.004 0.048 1802 Dihedral : 4.963 50.974 1467 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.55 % Allowed : 26.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.24), residues: 1285 helix: 1.48 (0.26), residues: 413 sheet: -0.25 (0.27), residues: 345 loop : -1.50 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 72 TYR 0.025 0.002 TYR S 235 PHE 0.016 0.002 PHE A 217 TRP 0.021 0.001 TRP S 47 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00502 (10566) covalent geometry : angle 0.63371 (14325) SS BOND : bond 0.00629 ( 6) SS BOND : angle 2.31795 ( 12) hydrogen bonds : bond 0.04899 ( 459) hydrogen bonds : angle 4.73728 ( 1332) *********************** 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 217 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 0.410 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: 0.5965 (m-80) cc_final: 0.5152 (m-80) REVERT: S 111 TRP cc_start: 0.7402 (m100) cc_final: 0.7163 (m-10) REVERT: S 141 THR cc_start: 0.5691 (m) cc_final: 0.5326 (p) REVERT: S 171 ASN cc_start: 0.7134 (m-40) cc_final: 0.6720 (m-40) REVERT: A 192 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: B 27 ASP cc_start: 0.7639 (t0) cc_final: 0.7375 (t0) REVERT: B 292 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: C 227 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8069 (pp) REVERT: C 306 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7596 (tp40) REVERT: C 309 ASP cc_start: 0.7759 (m-30) cc_final: 0.7491 (m-30) REVERT: G 32 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7810 (ttpp) REVERT: G 36 ASP cc_start: 0.7889 (m-30) cc_final: 0.7601 (m-30) REVERT: D 79 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6779 (tp) REVERT: D 83 LYS cc_start: 0.6781 (ptmm) cc_final: 0.6507 (pttm) REVERT: D 124 ASP cc_start: 0.8034 (t0) cc_final: 0.7684 (t0) REVERT: D 126 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7537 (p-80) outliers start: 62 outliers final: 40 residues processed: 200 average time/residue: 0.0979 time to fit residues: 28.2300 Evaluate side-chains 194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 58 ILE 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 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 298 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR 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 253 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 306 GLN 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 G residue 62 ARG 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 Chi-restraints excluded: chain D residue 126 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 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 = 0.4102 r_free = 0.4102 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119192 restraints weight = 13910.180| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.22 r_work: 0.3293 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10572 Z= 0.136 Angle : 0.575 7.805 14337 Z= 0.303 Chirality : 0.043 0.165 1605 Planarity : 0.004 0.054 1802 Dihedral : 4.842 52.317 1467 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.19 % Allowed : 28.74 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1285 helix: 1.63 (0.26), residues: 413 sheet: -0.18 (0.28), residues: 333 loop : -1.46 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.026 0.001 TYR S 235 PHE 0.014 0.001 PHE C 189 TRP 0.012 0.001 TRP A 75 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00311 (10566) covalent geometry : angle 0.57286 (14325) SS BOND : bond 0.00516 ( 6) SS BOND : angle 1.75015 ( 12) hydrogen bonds : bond 0.04151 ( 459) hydrogen bonds : angle 4.53099 ( 1332) *********************** 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 220 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.413 Fit side-chains 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: 0.5988 (m-80) cc_final: 0.5137 (m-80) REVERT: S 111 TRP cc_start: 0.7342 (m100) cc_final: 0.7124 (m-10) REVERT: S 141 THR cc_start: 0.5746 (m) cc_final: 0.5397 (p) REVERT: S 171 ASN cc_start: 0.7046 (m-40) cc_final: 0.6636 (m-40) REVERT: A 192 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: B 27 ASP cc_start: 0.7515 (t0) cc_final: 0.7284 (t0) REVERT: B 198 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8273 (mt) REVERT: B 292 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: C 227 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8049 (pp) REVERT: C 309 ASP cc_start: 0.7711 (m-30) cc_final: 0.7340 (m-30) REVERT: G 32 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7890 (ttpp) REVERT: G 36 ASP cc_start: 0.7830 (m-30) cc_final: 0.7586 (m-30) REVERT: D 45 PHE cc_start: 0.7419 (t80) cc_final: 0.7214 (t80) REVERT: D 79 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6764 (tp) REVERT: D 81 CYS cc_start: 0.6294 (t) cc_final: 0.5856 (t) REVERT: D 83 LYS cc_start: 0.6979 (ptmm) cc_final: 0.6736 (pttm) REVERT: D 124 ASP cc_start: 0.8058 (t0) cc_final: 0.7667 (t0) REVERT: D 126 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7548 (p-80) outliers start: 58 outliers final: 40 residues processed: 205 average time/residue: 0.0942 time to fit residues: 28.2017 Evaluate side-chains 207 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 172 THR 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 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 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR 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 182 THR 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 253 ILE 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 G residue 42 GLU Chi-restraints excluded: chain D residue 56 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 Chi-restraints excluded: chain D residue 126 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 B 259 GLN B 340 ASN D 11 GLN D 54 GLN D 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.169588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110627 restraints weight = 14331.596| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.19 r_work: 0.3179 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 10572 Z= 0.368 Angle : 0.764 9.786 14337 Z= 0.406 Chirality : 0.050 0.185 1605 Planarity : 0.005 0.052 1802 Dihedral : 5.532 50.635 1467 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 7.07 % Allowed : 28.56 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.23), residues: 1285 helix: 1.12 (0.26), residues: 406 sheet: -0.54 (0.27), residues: 346 loop : -1.66 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 180 TYR 0.030 0.003 TYR S 235 PHE 0.026 0.003 PHE A 217 TRP 0.020 0.002 TRP B 82 HIS 0.010 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00881 (10566) covalent geometry : angle 0.76048 (14325) SS BOND : bond 0.00954 ( 6) SS BOND : angle 2.61661 ( 12) hydrogen bonds : bond 0.06136 ( 459) hydrogen bonds : angle 5.19519 ( 1332) *********************** 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 228 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 149 time to evaluate : 0.397 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: S 18 ARG cc_start: 0.5971 (mmm-85) cc_final: 0.5660 (mmm-85) REVERT: S 141 THR cc_start: 0.5602 (m) cc_final: 0.5236 (p) REVERT: S 171 ASN cc_start: 0.7126 (m-40) cc_final: 0.6882 (m-40) REVERT: S 230 MET cc_start: 0.7153 (tmm) cc_final: 0.6820 (tmm) REVERT: A 192 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: A 268 TRP cc_start: 0.8411 (t60) cc_final: 0.8036 (t60) REVERT: B 27 ASP cc_start: 0.7845 (t0) cc_final: 0.7440 (t0) REVERT: B 215 GLU cc_start: 0.8319 (mp0) cc_final: 0.8119 (mp0) REVERT: B 292 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: C 227 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8084 (pp) REVERT: C 305 CYS cc_start: 0.8011 (t) cc_final: 0.7480 (t) REVERT: C 306 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: C 309 ASP cc_start: 0.7774 (m-30) cc_final: 0.7452 (m-30) REVERT: G 32 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7850 (ttpp) REVERT: G 36 ASP cc_start: 0.8046 (m-30) cc_final: 0.7743 (m-30) REVERT: D 124 ASP cc_start: 0.8102 (t0) cc_final: 0.7743 (t0) REVERT: D 126 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7669 (p-80) outliers start: 79 outliers final: 55 residues processed: 214 average time/residue: 0.0961 time to fit residues: 30.0439 Evaluate side-chains 205 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 37 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 145 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ILE 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 248 ILE 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 30 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 157 ILE 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 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 198 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 353 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 G residue 62 ARG Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 56 SER 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 97 CYS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 126 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 109 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 30 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN D 11 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 = 0.4107 r_free = 0.4107 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117897 restraints weight = 14067.860| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.11 r_work: 0.3335 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10572 Z= 0.116 Angle : 0.583 8.351 14337 Z= 0.308 Chirality : 0.042 0.151 1605 Planarity : 0.004 0.047 1802 Dihedral : 5.004 52.687 1467 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.21 % Allowed : 31.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.23), residues: 1285 helix: 1.50 (0.26), residues: 413 sheet: -0.26 (0.28), residues: 316 loop : -1.49 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.026 0.001 TYR S 235 PHE 0.038 0.001 PHE D 45 TRP 0.018 0.001 TRP A 75 HIS 0.010 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00251 (10566) covalent geometry : angle 0.58169 (14325) SS BOND : bond 0.00640 ( 6) SS BOND : angle 1.65241 ( 12) hydrogen bonds : bond 0.03955 ( 459) hydrogen bonds : angle 4.54439 ( 1332) *********************** 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 210 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.390 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 88 SER cc_start: 0.8928 (p) cc_final: 0.8680 (m) REVERT: S 141 THR cc_start: 0.5609 (m) cc_final: 0.5250 (p) REVERT: S 171 ASN cc_start: 0.7142 (m-40) cc_final: 0.6815 (m-40) REVERT: A 68 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8287 (ttpp) REVERT: A 192 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: A 236 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: B 27 ASP cc_start: 0.7667 (t0) cc_final: 0.7329 (t0) REVERT: B 198 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8347 (mt) REVERT: B 292 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: C 21 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6886 (mtm110) REVERT: C 227 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8056 (pp) REVERT: C 309 ASP cc_start: 0.7783 (m-30) cc_final: 0.7420 (m-30) REVERT: G 32 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7975 (ttpp) REVERT: G 36 ASP cc_start: 0.7861 (m-30) cc_final: 0.7655 (m-30) REVERT: D 79 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7029 (tp) REVERT: D 83 LYS cc_start: 0.7221 (ptmm) cc_final: 0.7016 (pttm) REVERT: D 124 ASP cc_start: 0.8051 (t0) cc_final: 0.7626 (t0) REVERT: D 126 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7586 (p-80) outliers start: 47 outliers final: 29 residues processed: 197 average time/residue: 0.1022 time to fit residues: 28.7243 Evaluate side-chains 190 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 168 SER 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 192 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 250 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 146 LEU 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 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 G residue 25 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 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 126 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 121 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 9 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118677 restraints weight = 14078.947| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.10 r_work: 0.3348 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10572 Z= 0.112 Angle : 0.566 8.130 14337 Z= 0.298 Chirality : 0.042 0.152 1605 Planarity : 0.004 0.054 1802 Dihedral : 4.823 52.893 1467 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.21 % Allowed : 31.87 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.24), residues: 1285 helix: 1.62 (0.26), residues: 413 sheet: -0.25 (0.28), residues: 321 loop : -1.40 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.027 0.001 TYR S 235 PHE 0.034 0.001 PHE D 45 TRP 0.011 0.001 TRP A 75 HIS 0.010 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00247 (10566) covalent geometry : angle 0.56335 (14325) SS BOND : bond 0.00657 ( 6) SS BOND : angle 1.93633 ( 12) hydrogen bonds : bond 0.03795 ( 459) hydrogen bonds : angle 4.37117 ( 1332) *********************** 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 195 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.440 Fit side-chains 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: 0.5948 (m-80) cc_final: 0.5122 (m-80) REVERT: S 88 SER cc_start: 0.8894 (p) cc_final: 0.8651 (m) REVERT: S 171 ASN cc_start: 0.7191 (m-40) cc_final: 0.6904 (m-40) REVERT: A 192 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: B 27 ASP cc_start: 0.7636 (t0) cc_final: 0.7375 (t0) REVERT: B 292 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: C 309 ASP cc_start: 0.7725 (m-30) cc_final: 0.7353 (m-30) REVERT: G 32 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7991 (ttpp) REVERT: D 124 ASP cc_start: 0.8027 (t0) cc_final: 0.7613 (t0) REVERT: D 126 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7496 (p-80) outliers start: 47 outliers final: 34 residues processed: 181 average time/residue: 0.0966 time to fit residues: 25.4562 Evaluate side-chains 187 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 23 SER 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 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 298 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU 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 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 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 126 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117033 restraints weight = 13891.094| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.20 r_work: 0.3255 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10572 Z= 0.170 Angle : 0.607 9.194 14337 Z= 0.318 Chirality : 0.043 0.157 1605 Planarity : 0.004 0.047 1802 Dihedral : 4.897 52.794 1467 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.30 % Allowed : 31.87 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.24), residues: 1285 helix: 1.55 (0.26), residues: 414 sheet: -0.38 (0.27), residues: 340 loop : -1.42 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.028 0.002 TYR S 235 PHE 0.030 0.002 PHE D 45 TRP 0.013 0.001 TRP S 47 HIS 0.009 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00401 (10566) covalent geometry : angle 0.60388 (14325) SS BOND : bond 0.00579 ( 6) SS BOND : angle 2.05683 ( 12) hydrogen bonds : bond 0.04377 ( 459) hydrogen bonds : angle 4.45248 ( 1332) *********************** 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 194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.398 Fit side-chains 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: 0.5916 (m-80) cc_final: 0.5124 (m-80) REVERT: S 88 SER cc_start: 0.8858 (p) cc_final: 0.8601 (m) REVERT: S 171 ASN cc_start: 0.7112 (m-40) cc_final: 0.6890 (m-40) REVERT: A 192 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: A 268 TRP cc_start: 0.8287 (t60) cc_final: 0.7938 (t60) REVERT: B 27 ASP cc_start: 0.7605 (t0) cc_final: 0.7378 (t0) REVERT: B 292 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: B 314 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7727 (ptm160) REVERT: C 309 ASP cc_start: 0.7648 (m-30) cc_final: 0.7251 (m-30) REVERT: G 32 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7936 (ttpp) REVERT: D 124 ASP cc_start: 0.7974 (t0) cc_final: 0.7541 (t0) REVERT: D 126 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7485 (p-80) outliers start: 48 outliers final: 38 residues processed: 181 average time/residue: 0.1009 time to fit residues: 26.2877 Evaluate side-chains 187 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 23 SER 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 192 GLN 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 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR 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 B residue 314 ARG 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 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 G residue 42 GLU 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 126 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 192 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.177944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.119930 restraints weight = 13702.306| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.20 r_work: 0.3293 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10572 Z= 0.120 Angle : 0.586 9.248 14337 Z= 0.305 Chirality : 0.042 0.150 1605 Planarity : 0.004 0.051 1802 Dihedral : 4.788 53.354 1467 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.21 % Allowed : 32.14 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1285 helix: 1.68 (0.26), residues: 414 sheet: -0.20 (0.28), residues: 323 loop : -1.39 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.026 0.001 TYR S 235 PHE 0.030 0.001 PHE D 45 TRP 0.013 0.001 TRP A 75 HIS 0.008 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00270 (10566) covalent geometry : angle 0.58415 (14325) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.78784 ( 12) hydrogen bonds : bond 0.03872 ( 459) hydrogen bonds : angle 4.32961 ( 1332) ********************** 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 198 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.384 Fit side-chains 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: 0.5919 (m-80) cc_final: 0.5105 (m-80) REVERT: S 88 SER cc_start: 0.8775 (p) cc_final: 0.8512 (m) REVERT: A 268 TRP cc_start: 0.8188 (t60) cc_final: 0.7825 (t60) REVERT: B 259 GLN cc_start: 0.8143 (mt0) cc_final: 0.7665 (mt0) REVERT: B 292 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 314 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7620 (ptm160) REVERT: C 227 LEU cc_start: 0.8410 (pp) cc_final: 0.8113 (pp) REVERT: C 309 ASP cc_start: 0.7662 (m-30) cc_final: 0.7266 (m-30) REVERT: G 32 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7953 (ttpp) REVERT: G 36 ASP cc_start: 0.7891 (m-30) cc_final: 0.7594 (m-30) REVERT: D 124 ASP cc_start: 0.7953 (t0) cc_final: 0.7506 (t0) REVERT: D 126 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7420 (p-80) outliers start: 47 outliers final: 41 residues processed: 185 average time/residue: 0.0994 time to fit residues: 26.4249 Evaluate side-chains 194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain A residue 23 SER 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 180 GLU 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 256 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU 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 B residue 314 ARG 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 C residue 314 LYS 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 G residue 42 GLU 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 126 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 108 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118516 restraints weight = 13968.577| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.20 r_work: 0.3276 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10572 Z= 0.146 Angle : 0.608 10.797 14337 Z= 0.318 Chirality : 0.043 0.152 1605 Planarity : 0.004 0.053 1802 Dihedral : 4.793 53.258 1467 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.48 % Allowed : 31.78 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1285 helix: 1.68 (0.26), residues: 413 sheet: -0.28 (0.27), residues: 336 loop : -1.33 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.027 0.001 TYR S 235 PHE 0.028 0.001 PHE D 45 TRP 0.011 0.001 TRP S 47 HIS 0.010 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00340 (10566) covalent geometry : angle 0.60560 (14325) SS BOND : bond 0.00550 ( 6) SS BOND : angle 1.86474 ( 12) hydrogen bonds : bond 0.04066 ( 459) hydrogen bonds : angle 4.35454 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.71 seconds wall clock time: 53 minutes 17.03 seconds (3197.03 seconds total)