Starting phenix.real_space_refine on Mon May 12 09:22:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgu_38332/05_2025/8xgu_38332.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 62 5.16 5 C 5603 2.51 5 N 1521 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8799 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2231 Classifications: {'peptide': 287} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 269} Chain breaks: 1 Chain: "C" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1697 Classifications: {'peptide': 213} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} 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: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 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: {'PCIS': 1, 'PTRANS': 9, '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: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Unusual residues: {'ACE': 1, 'XZA': 1} Classifications: {'peptide': 8, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'ACE_C-N': 1, 'CIS': 2, 'TRANS': 4, None: 2} Not linked: pdbres="PHE E 6 " pdbres="XZA E 7 " Not linked: pdbres="XZA E 7 " pdbres="LEU E 8 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NMM:plan-2': 1, 'HZP:plan-1': 1, 'XZA:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.64 Number of scatterers: 8799 At special positions: 0 Unit cell: (93.5, 122.4, 128.35, 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 62 16.00 O 1613 8.00 N 1521 7.00 C 5603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY E 2 " Input volumes are d-peptide like pdb=" CB NMM E 9 " pdb=" CB TRP E 10 " Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 17 sheets defined 36.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 45 through 70 removed outlier: 4.040A pdb=" N PHE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 101 Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 111 through 146 removed outlier: 3.514A pdb=" N CYS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 197 through 234 Proline residue: A 216 - end of helix removed outlier: 3.623A pdb=" N VAL A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 276 removed outlier: 3.635A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.903A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.767A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.570A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.814A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.868A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.511A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.524A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.709A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.600A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.185A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191 removed outlier: 7.033A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.042A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.906A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.853A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.023A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.067A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.712A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.635A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.651A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.164A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AB3, first strand: chain 'S' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.536A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'S' and resid 174 through 175 Processing sheet with id=AB7, first strand: chain 'S' and resid 185 through 186 Processing sheet with id=AB8, first strand: chain 'S' and resid 189 through 190 412 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1406 1.30 - 1.43: 2458 1.43 - 1.56: 5024 1.56 - 1.69: 12 1.69 - 1.83: 88 Bond restraints: 8988 Sorted by residual: bond pdb=" C NMM E 9 " pdb=" N TRP E 10 " ideal model delta sigma weight residual 1.329 1.512 -0.183 1.40e-02 5.10e+03 1.72e+02 bond pdb=" C ASN E 4 " pdb=" N THR E 5 " ideal model delta sigma weight residual 1.329 1.510 -0.181 1.40e-02 5.10e+03 1.68e+02 bond pdb=" C HZP E 3 " pdb=" N ASN E 4 " ideal model delta sigma weight residual 1.329 1.492 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" C LEU E 8 " pdb=" N NMM E 9 " ideal model delta sigma weight residual 1.329 1.483 -0.154 1.40e-02 5.10e+03 1.21e+02 bond pdb=" C THR E 5 " pdb=" N PHE E 6 " ideal model delta sigma weight residual 1.329 1.468 -0.139 1.40e-02 5.10e+03 9.80e+01 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11771 1.52 - 3.03: 311 3.03 - 4.55: 65 4.55 - 6.06: 33 6.06 - 7.58: 6 Bond angle restraints: 12186 Sorted by residual: angle pdb=" CA ASN E 4 " pdb=" CB ASN E 4 " pdb=" CG ASN E 4 " ideal model delta sigma weight residual 112.60 118.60 -6.00 1.00e+00 1.00e+00 3.60e+01 angle pdb=" CA ASN E 4 " pdb=" C ASN E 4 " pdb=" N THR E 5 " ideal model delta sigma weight residual 116.20 123.50 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" O ASN E 4 " pdb=" C ASN E 4 " pdb=" N THR E 5 " ideal model delta sigma weight residual 123.00 117.82 5.18 1.60e+00 3.91e-01 1.05e+01 angle pdb=" C LEU A 47 " pdb=" N PHE A 48 " pdb=" CA PHE A 48 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.79e+00 ... (remaining 12181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4802 16.23 - 32.46: 397 32.46 - 48.69: 83 48.69 - 64.92: 13 64.92 - 81.15: 10 Dihedral angle restraints: 5305 sinusoidal: 2028 harmonic: 3277 Sorted by residual: dihedral pdb=" CA PHE A 48 " pdb=" C PHE A 48 " pdb=" N PHE A 49 " pdb=" CA PHE A 49 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA SER A 184 " pdb=" C SER A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU A 252 " pdb=" C GLU A 252 " pdb=" N ARG A 253 " pdb=" CA ARG A 253 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 1377 1.045 - 2.090: 0 2.090 - 3.135: 0 3.135 - 4.180: 0 4.180 - 5.225: 3 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB THR E 5 " pdb=" CA THR E 5 " pdb=" OG1 THR E 5 " pdb=" CG2 THR E 5 " both_signs ideal model delta sigma weight residual False 2.55 -2.67 5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" CA TRP E 10 " pdb=" N TRP E 10 " pdb=" C TRP E 10 " pdb=" CB TRP E 10 " both_signs ideal model delta sigma weight residual False 2.51 -2.27 4.78 2.00e-01 2.50e+01 5.71e+02 chirality pdb=" CA NMM E 9 " pdb=" N NMM E 9 " pdb=" C NMM E 9 " pdb=" CB NMM E 9 " both_signs ideal model delta sigma weight residual False 2.51 -2.10 4.61 2.00e-01 2.50e+01 5.30e+02 ... (remaining 1377 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 48 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C PHE A 48 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 48 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 49 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 186 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO A 187 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 211 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA A 211 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA A 211 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 212 " -0.013 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 142 2.67 - 3.23: 8350 3.23 - 3.78: 13524 3.78 - 4.34: 17830 4.34 - 4.90: 30201 Nonbonded interactions: 70047 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.111 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 192 " pdb=" OE1 GLU A 193 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O ALA A 273 " model vdw 2.188 3.040 ... (remaining 70042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:9.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.195 8994 Z= 0.439 Angle : 0.662 7.581 12192 Z= 0.351 Chirality : 0.232 5.225 1380 Planarity : 0.004 0.063 1541 Dihedral : 13.143 81.153 3184 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.21 % Allowed : 0.54 % Favored : 99.25 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1105 helix: 1.62 (0.28), residues: 374 sheet: -0.82 (0.30), residues: 289 loop : -1.35 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 43 HIS 0.004 0.001 HIS A 181 PHE 0.012 0.001 PHE A 195 TYR 0.021 0.001 TYR A 313 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.12514 ( 412) hydrogen bonds : angle 5.23935 ( 1158) SS BOND : bond 0.00630 ( 3) SS BOND : angle 1.21138 ( 6) covalent geometry : bond 0.00761 ( 8988) covalent geometry : angle 0.66153 (12186) Misc. bond : bond 0.03317 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.031 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 43 TRP cc_start: 0.8194 (p-90) cc_final: 0.7964 (p-90) REVERT: A 193 GLU cc_start: 0.8375 (mp0) cc_final: 0.8152 (OUTLIER) REVERT: A 295 HIS cc_start: 0.8356 (t70) cc_final: 0.8129 (t70) REVERT: C 306 GLN cc_start: 0.8659 (mm110) cc_final: 0.8263 (mm110) REVERT: B 59 TYR cc_start: 0.8493 (m-80) cc_final: 0.8223 (m-80) REVERT: B 175 GLN cc_start: 0.8300 (mm110) cc_final: 0.8095 (mm-40) REVERT: B 259 GLN cc_start: 0.8382 (pt0) cc_final: 0.8151 (pt0) REVERT: B 262 MET cc_start: 0.8568 (mmt) cc_final: 0.8103 (mpp) REVERT: G 21 MET cc_start: 0.8942 (tmm) cc_final: 0.8718 (tmm) REVERT: E 5 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6653 (p) outliers start: 2 outliers final: 2 residues processed: 190 average time/residue: 1.1601 time to fit residues: 235.3461 Evaluate side-chains 145 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN B 110 ASN B 340 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN E 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079857 restraints weight = 16540.103| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.41 r_work: 0.3003 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8994 Z= 0.146 Angle : 0.697 12.233 12192 Z= 0.347 Chirality : 0.050 0.701 1380 Planarity : 0.005 0.057 1541 Dihedral : 5.693 70.264 1241 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.18 % Allowed : 12.88 % Favored : 85.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1105 helix: 1.48 (0.27), residues: 387 sheet: -0.76 (0.30), residues: 288 loop : -1.31 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 43 HIS 0.003 0.001 HIS A 181 PHE 0.012 0.001 PHE E 6 TYR 0.033 0.001 TYR A 313 ARG 0.008 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 412) hydrogen bonds : angle 4.53904 ( 1158) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.26066 ( 6) covalent geometry : bond 0.00323 ( 8988) covalent geometry : angle 0.69699 (12186) Misc. bond : bond 0.00119 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.945 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 114 MET cc_start: 0.6929 (mmp) cc_final: 0.6346 (tpp) REVERT: A 193 GLU cc_start: 0.8644 (mp0) cc_final: 0.8279 (pp20) REVERT: A 295 HIS cc_start: 0.8493 (t70) cc_final: 0.8247 (t70) REVERT: C 306 GLN cc_start: 0.8840 (mm110) cc_final: 0.8428 (mm110) REVERT: C 313 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8746 (ptp-110) REVERT: B 19 ARG cc_start: 0.8000 (ppt90) cc_final: 0.7653 (ppt170) REVERT: B 130 GLU cc_start: 0.8374 (mp0) cc_final: 0.8069 (mp0) REVERT: B 259 GLN cc_start: 0.8445 (pt0) cc_final: 0.8205 (pt0) REVERT: B 262 MET cc_start: 0.9021 (mmt) cc_final: 0.8705 (tpp) REVERT: S 83 MET cc_start: 0.8276 (mmt) cc_final: 0.7918 (mmt) outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 1.2409 time to fit residues: 217.4544 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077283 restraints weight = 16693.818| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.28 r_work: 0.2996 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8994 Z= 0.242 Angle : 0.725 11.850 12192 Z= 0.367 Chirality : 0.050 0.578 1380 Planarity : 0.005 0.055 1541 Dihedral : 5.377 62.836 1237 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.72 % Allowed : 17.49 % Favored : 80.79 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1105 helix: 1.38 (0.27), residues: 390 sheet: -0.76 (0.30), residues: 283 loop : -1.34 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 43 HIS 0.004 0.001 HIS A 329 PHE 0.014 0.002 PHE B 199 TYR 0.014 0.002 TYR A 313 ARG 0.007 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 412) hydrogen bonds : angle 4.64754 ( 1158) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.36605 ( 6) covalent geometry : bond 0.00569 ( 8988) covalent geometry : angle 0.72452 (12186) Misc. bond : bond 0.00067 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.965 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 193 GLU cc_start: 0.8653 (mp0) cc_final: 0.8241 (pp20) REVERT: A 295 HIS cc_start: 0.8446 (t70) cc_final: 0.8200 (t70) REVERT: C 313 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8797 (ptp-110) REVERT: B 130 GLU cc_start: 0.8596 (mp0) cc_final: 0.8360 (mp0) REVERT: B 215 GLU cc_start: 0.8744 (mp0) cc_final: 0.8534 (mp0) REVERT: B 259 GLN cc_start: 0.8546 (pt0) cc_final: 0.8271 (pt0) REVERT: B 262 MET cc_start: 0.8985 (mmt) cc_final: 0.8686 (tpp) REVERT: G 18 GLN cc_start: 0.7869 (tp40) cc_final: 0.7642 (tp40) REVERT: G 21 MET cc_start: 0.8949 (tmm) cc_final: 0.8674 (tmt) REVERT: G 22 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7779 (tm-30) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 1.3102 time to fit residues: 209.9323 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 208 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** S 142 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 = 0.3686 r_free = 0.3686 target = 0.110858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079287 restraints weight = 16288.238| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.27 r_work: 0.3028 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8994 Z= 0.147 Angle : 0.685 11.954 12192 Z= 0.343 Chirality : 0.048 0.547 1380 Planarity : 0.005 0.057 1541 Dihedral : 5.089 53.758 1237 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.39 % Allowed : 19.10 % Favored : 79.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1105 helix: 1.48 (0.27), residues: 389 sheet: -0.73 (0.30), residues: 289 loop : -1.39 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 43 HIS 0.003 0.001 HIS A 329 PHE 0.012 0.001 PHE E 6 TYR 0.012 0.001 TYR A 65 ARG 0.010 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 412) hydrogen bonds : angle 4.50373 ( 1158) SS BOND : bond 0.00457 ( 3) SS BOND : angle 1.08189 ( 6) covalent geometry : bond 0.00333 ( 8988) covalent geometry : angle 0.68515 (12186) Misc. bond : bond 0.00015 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.024 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 114 MET cc_start: 0.6943 (mmp) cc_final: 0.6485 (tpp) REVERT: A 295 HIS cc_start: 0.8407 (t70) cc_final: 0.8161 (t70) REVERT: C 313 ARG cc_start: 0.9007 (ttm110) cc_final: 0.8799 (ptp-110) REVERT: B 19 ARG cc_start: 0.8326 (tmm160) cc_final: 0.8110 (tmm160) REVERT: B 130 GLU cc_start: 0.8598 (mp0) cc_final: 0.8375 (mp0) REVERT: B 215 GLU cc_start: 0.8733 (mp0) cc_final: 0.8510 (mp0) REVERT: B 259 GLN cc_start: 0.8495 (pt0) cc_final: 0.8225 (pt0) REVERT: B 262 MET cc_start: 0.8988 (mmt) cc_final: 0.8689 (tpp) REVERT: G 18 GLN cc_start: 0.7921 (tp40) cc_final: 0.7641 (tp40) REVERT: G 21 MET cc_start: 0.8948 (tmm) cc_final: 0.8702 (tmt) REVERT: G 22 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7741 (tm-30) REVERT: S 144 THR cc_start: 0.7412 (OUTLIER) cc_final: 0.7103 (p) outliers start: 13 outliers final: 6 residues processed: 154 average time/residue: 1.2922 time to fit residues: 211.3817 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 0.0030 chunk 44 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080584 restraints weight = 16254.965| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.28 r_work: 0.3059 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8994 Z= 0.130 Angle : 0.689 12.030 12192 Z= 0.344 Chirality : 0.047 0.538 1380 Planarity : 0.004 0.057 1541 Dihedral : 4.827 52.186 1237 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.82 % Allowed : 19.96 % Favored : 78.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1105 helix: 1.51 (0.28), residues: 387 sheet: -0.65 (0.30), residues: 288 loop : -1.37 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 43 HIS 0.001 0.000 HIS A 295 PHE 0.013 0.001 PHE E 6 TYR 0.015 0.001 TYR A 313 ARG 0.012 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 412) hydrogen bonds : angle 4.46166 ( 1158) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.99030 ( 6) covalent geometry : bond 0.00290 ( 8988) covalent geometry : angle 0.68853 (12186) Misc. bond : bond 0.00011 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 114 MET cc_start: 0.6927 (mmp) cc_final: 0.6424 (tpp) REVERT: A 295 HIS cc_start: 0.8418 (t70) cc_final: 0.8186 (t70) REVERT: B 19 ARG cc_start: 0.8350 (tmm160) cc_final: 0.7887 (tmm160) REVERT: B 20 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8549 (m-30) REVERT: B 74 SER cc_start: 0.8875 (t) cc_final: 0.8635 (p) REVERT: B 130 GLU cc_start: 0.8581 (mp0) cc_final: 0.8371 (mp0) REVERT: B 215 GLU cc_start: 0.8716 (mp0) cc_final: 0.8494 (mp0) REVERT: B 259 GLN cc_start: 0.8455 (pt0) cc_final: 0.8213 (pt0) REVERT: B 262 MET cc_start: 0.8967 (mmt) cc_final: 0.8664 (tpp) REVERT: G 18 GLN cc_start: 0.7875 (tp40) cc_final: 0.7562 (tp40) REVERT: G 21 MET cc_start: 0.9012 (tmm) cc_final: 0.8759 (tmt) REVERT: G 22 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7735 (tm-30) REVERT: S 144 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7102 (p) REVERT: S 218 ARG cc_start: 0.8256 (mmp80) cc_final: 0.7959 (mmp80) outliers start: 17 outliers final: 7 residues processed: 167 average time/residue: 1.1746 time to fit residues: 209.0991 Evaluate side-chains 158 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** S 142 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 = 0.3705 r_free = 0.3705 target = 0.112344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080933 restraints weight = 16153.043| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.26 r_work: 0.3062 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.134 Angle : 0.702 12.130 12192 Z= 0.347 Chirality : 0.048 0.538 1380 Planarity : 0.005 0.055 1541 Dihedral : 4.704 51.337 1237 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.82 % Allowed : 21.14 % Favored : 77.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1105 helix: 1.52 (0.28), residues: 387 sheet: -0.61 (0.30), residues: 289 loop : -1.32 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 43 HIS 0.003 0.001 HIS C 188 PHE 0.016 0.001 PHE E 6 TYR 0.028 0.001 TYR A 190 ARG 0.012 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 412) hydrogen bonds : angle 4.42779 ( 1158) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.90132 ( 6) covalent geometry : bond 0.00301 ( 8988) covalent geometry : angle 0.70155 (12186) Misc. bond : bond 0.00010 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.069 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 73 MET cc_start: 0.7384 (mmp) cc_final: 0.6615 (mmp) REVERT: A 114 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6433 (tpp) REVERT: A 295 HIS cc_start: 0.8420 (t70) cc_final: 0.8182 (t70) REVERT: B 19 ARG cc_start: 0.8359 (tmm160) cc_final: 0.7856 (tmm160) REVERT: B 20 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: B 130 GLU cc_start: 0.8578 (mp0) cc_final: 0.8368 (mp0) REVERT: B 215 GLU cc_start: 0.8754 (mp0) cc_final: 0.8524 (mp0) REVERT: B 262 MET cc_start: 0.8965 (mmt) cc_final: 0.8683 (tpp) REVERT: G 18 GLN cc_start: 0.7855 (tp40) cc_final: 0.7544 (tp40) REVERT: G 21 MET cc_start: 0.8902 (tmm) cc_final: 0.8548 (tmt) REVERT: G 22 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7672 (tm-30) REVERT: G 47 GLU cc_start: 0.8624 (mp0) cc_final: 0.8182 (tm-30) REVERT: S 83 MET cc_start: 0.8366 (mmt) cc_final: 0.7989 (tpp) REVERT: S 144 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7205 (p) REVERT: S 218 ARG cc_start: 0.8219 (mmp80) cc_final: 0.7881 (mmp80) outliers start: 17 outliers final: 6 residues processed: 158 average time/residue: 1.2430 time to fit residues: 209.4986 Evaluate side-chains 150 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080596 restraints weight = 16290.952| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.26 r_work: 0.3052 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8994 Z= 0.144 Angle : 0.718 12.175 12192 Z= 0.356 Chirality : 0.048 0.538 1380 Planarity : 0.005 0.058 1541 Dihedral : 4.729 50.734 1237 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.68 % Allowed : 21.46 % Favored : 75.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1105 helix: 1.58 (0.28), residues: 381 sheet: -0.58 (0.31), residues: 281 loop : -1.35 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 43 HIS 0.002 0.001 HIS A 329 PHE 0.012 0.001 PHE E 6 TYR 0.025 0.001 TYR A 190 ARG 0.012 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 412) hydrogen bonds : angle 4.44916 ( 1158) SS BOND : bond 0.00441 ( 3) SS BOND : angle 0.92379 ( 6) covalent geometry : bond 0.00328 ( 8988) covalent geometry : angle 0.71817 (12186) Misc. bond : bond 0.00020 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.079 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 73 MET cc_start: 0.7430 (mmp) cc_final: 0.6705 (mmp) REVERT: A 114 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6468 (tpp) REVERT: A 295 HIS cc_start: 0.8441 (t70) cc_final: 0.8200 (t70) REVERT: B 19 ARG cc_start: 0.8372 (tmm160) cc_final: 0.7838 (tmm160) REVERT: B 20 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: B 32 GLN cc_start: 0.8984 (mp10) cc_final: 0.8753 (mp10) REVERT: B 130 GLU cc_start: 0.8581 (mp0) cc_final: 0.8358 (mp0) REVERT: G 18 GLN cc_start: 0.7830 (tp40) cc_final: 0.7578 (tp40) REVERT: G 21 MET cc_start: 0.8866 (tmm) cc_final: 0.8523 (tmt) REVERT: G 22 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7650 (tm-30) REVERT: G 47 GLU cc_start: 0.8614 (mp0) cc_final: 0.8168 (tm-30) REVERT: S 83 MET cc_start: 0.8386 (mmt) cc_final: 0.8003 (tpp) REVERT: S 144 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7221 (p) REVERT: S 218 ARG cc_start: 0.8223 (mmp80) cc_final: 0.7868 (mmp80) REVERT: E 5 THR cc_start: 0.8182 (m) cc_final: 0.7975 (p) outliers start: 25 outliers final: 7 residues processed: 160 average time/residue: 1.2439 time to fit residues: 211.9903 Evaluate side-chains 154 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** S 142 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 = 0.3697 r_free = 0.3697 target = 0.111765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080230 restraints weight = 16386.833| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.26 r_work: 0.3049 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8994 Z= 0.154 Angle : 0.748 12.206 12192 Z= 0.367 Chirality : 0.049 0.537 1380 Planarity : 0.005 0.063 1541 Dihedral : 4.739 50.178 1237 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.25 % Allowed : 22.10 % Favored : 75.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1105 helix: 1.53 (0.28), residues: 381 sheet: -0.52 (0.31), residues: 272 loop : -1.42 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 43 HIS 0.002 0.001 HIS S 232 PHE 0.009 0.001 PHE E 6 TYR 0.025 0.001 TYR A 190 ARG 0.014 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 412) hydrogen bonds : angle 4.48243 ( 1158) SS BOND : bond 0.00440 ( 3) SS BOND : angle 0.94996 ( 6) covalent geometry : bond 0.00354 ( 8988) covalent geometry : angle 0.74807 (12186) Misc. bond : bond 0.00024 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.989 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 73 MET cc_start: 0.7472 (mmt) cc_final: 0.6743 (mmp) REVERT: A 114 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6458 (tpp) REVERT: A 295 HIS cc_start: 0.8442 (t70) cc_final: 0.8204 (t70) REVERT: B 32 GLN cc_start: 0.9032 (mp10) cc_final: 0.8763 (mp10) REVERT: B 130 GLU cc_start: 0.8575 (mp0) cc_final: 0.8360 (mp0) REVERT: G 18 GLN cc_start: 0.7890 (tp40) cc_final: 0.7656 (tp40) REVERT: G 21 MET cc_start: 0.8901 (tmm) cc_final: 0.8589 (tmt) REVERT: G 22 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7709 (tm-30) REVERT: G 47 GLU cc_start: 0.8608 (mp0) cc_final: 0.8168 (tm-30) REVERT: S 83 MET cc_start: 0.8398 (mmt) cc_final: 0.7999 (tpp) REVERT: S 144 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (p) REVERT: S 218 ARG cc_start: 0.8232 (mmp80) cc_final: 0.7872 (mmp80) outliers start: 21 outliers final: 10 residues processed: 163 average time/residue: 1.2447 time to fit residues: 215.5411 Evaluate side-chains 156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079792 restraints weight = 16631.872| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.37 r_work: 0.3003 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8994 Z= 0.147 Angle : 0.776 12.230 12192 Z= 0.381 Chirality : 0.049 0.531 1380 Planarity : 0.005 0.065 1541 Dihedral : 4.732 49.530 1237 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.39 % Allowed : 23.39 % Favored : 75.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1105 helix: 1.46 (0.28), residues: 387 sheet: -0.54 (0.31), residues: 272 loop : -1.41 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 43 HIS 0.002 0.001 HIS A 329 PHE 0.012 0.001 PHE E 6 TYR 0.029 0.001 TYR A 190 ARG 0.014 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 412) hydrogen bonds : angle 4.54456 ( 1158) SS BOND : bond 0.00408 ( 3) SS BOND : angle 0.94186 ( 6) covalent geometry : bond 0.00338 ( 8988) covalent geometry : angle 0.77635 (12186) Misc. bond : bond 0.00017 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.010 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 73 MET cc_start: 0.7410 (mmt) cc_final: 0.6714 (mmp) REVERT: A 114 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6379 (tpp) REVERT: A 295 HIS cc_start: 0.8515 (t70) cc_final: 0.8295 (t70) REVERT: B 32 GLN cc_start: 0.9001 (mp10) cc_final: 0.8768 (mp10) REVERT: B 130 GLU cc_start: 0.8486 (mp0) cc_final: 0.8259 (mp0) REVERT: G 13 ARG cc_start: 0.8581 (pmt170) cc_final: 0.7642 (pmm-80) REVERT: G 17 GLU cc_start: 0.9463 (tp30) cc_final: 0.9062 (pm20) REVERT: G 18 GLN cc_start: 0.7809 (tp40) cc_final: 0.7484 (tp40) REVERT: G 21 MET cc_start: 0.8863 (tmm) cc_final: 0.8440 (tmt) REVERT: G 22 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7616 (tm-30) REVERT: G 47 GLU cc_start: 0.8579 (mp0) cc_final: 0.8108 (tm-30) REVERT: S 83 MET cc_start: 0.8475 (mmt) cc_final: 0.8057 (tpp) REVERT: S 144 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7134 (p) REVERT: S 218 ARG cc_start: 0.8146 (mmp80) cc_final: 0.7782 (mmp80) outliers start: 13 outliers final: 9 residues processed: 152 average time/residue: 1.3664 time to fit residues: 221.4374 Evaluate side-chains 156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** S 142 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 = 0.3647 r_free = 0.3647 target = 0.110666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079049 restraints weight = 16662.512| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.39 r_work: 0.2990 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8994 Z= 0.162 Angle : 0.793 12.296 12192 Z= 0.386 Chirality : 0.049 0.536 1380 Planarity : 0.005 0.069 1541 Dihedral : 4.762 48.919 1237 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.50 % Allowed : 23.50 % Favored : 75.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1105 helix: 1.44 (0.28), residues: 387 sheet: -0.59 (0.31), residues: 274 loop : -1.41 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 43 HIS 0.003 0.001 HIS C 188 PHE 0.012 0.001 PHE B 292 TYR 0.024 0.001 TYR A 190 ARG 0.014 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 412) hydrogen bonds : angle 4.57524 ( 1158) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.99757 ( 6) covalent geometry : bond 0.00377 ( 8988) covalent geometry : angle 0.79308 (12186) Misc. bond : bond 0.00021 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.922 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 114 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6405 (tpp) REVERT: A 190 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: A 295 HIS cc_start: 0.8511 (t70) cc_final: 0.8295 (t70) REVERT: B 32 GLN cc_start: 0.9059 (mp10) cc_final: 0.8714 (pm20) REVERT: B 130 GLU cc_start: 0.8485 (mp0) cc_final: 0.8254 (mp0) REVERT: G 13 ARG cc_start: 0.8570 (pmt170) cc_final: 0.7925 (pmm-80) REVERT: G 17 GLU cc_start: 0.9444 (tp30) cc_final: 0.8985 (pt0) REVERT: G 18 GLN cc_start: 0.7821 (tp40) cc_final: 0.7531 (tp40) REVERT: G 21 MET cc_start: 0.8851 (tmm) cc_final: 0.8455 (tmt) REVERT: G 22 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7569 (tm-30) REVERT: G 47 GLU cc_start: 0.8550 (mp0) cc_final: 0.8071 (tm-30) REVERT: S 144 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7176 (p) REVERT: S 218 ARG cc_start: 0.8146 (mmp80) cc_final: 0.7761 (mmp80) outliers start: 14 outliers final: 9 residues processed: 150 average time/residue: 1.2540 time to fit residues: 199.6526 Evaluate side-chains 151 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080213 restraints weight = 16648.586| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.40 r_work: 0.3012 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8994 Z= 0.142 Angle : 0.789 12.258 12192 Z= 0.382 Chirality : 0.048 0.519 1380 Planarity : 0.005 0.065 1541 Dihedral : 4.678 48.174 1237 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.39 % Allowed : 23.71 % Favored : 74.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1105 helix: 1.44 (0.28), residues: 387 sheet: -0.58 (0.31), residues: 274 loop : -1.39 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 43 HIS 0.002 0.000 HIS A 329 PHE 0.013 0.001 PHE E 6 TYR 0.026 0.001 TYR C 296 ARG 0.015 0.001 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 412) hydrogen bonds : angle 4.54781 ( 1158) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.90877 ( 6) covalent geometry : bond 0.00327 ( 8988) covalent geometry : angle 0.78848 (12186) Misc. bond : bond 0.00015 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6325.65 seconds wall clock time: 109 minutes 39.74 seconds (6579.74 seconds total)