Starting phenix.real_space_refine on Wed Jan 15 23:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgu_38332/01_2025/8xgu_38332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgu_38332/01_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_38332/01_2025/8xgu_38332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgu_38332/01_2025/8xgu_38332.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgu_38332/01_2025/8xgu_38332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgu_38332/01_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-5571/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: 5.89, per 1000 atoms: 0.67 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: 2.59 Conformation dependent library (CDL) restraints added in 976.0 milliseconds 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: 0.99 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: 2.45 Time building geometry restraints manager: 2.79 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: 1.370 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.730 Find NCS groups from input model: 0.110 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- 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 8988 Z= 0.560 Angle : 0.662 7.581 12186 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 *********************** 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 : 1.011 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: 1.2204 time to fit residues: 247.3412 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 : 0.977 ------------------------------------------------------------------------------- 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 8988 Z= 0.209 Angle : 0.697 12.233 12186 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 *********************** 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 : 0.949 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: 1.3526 time to fit residues: 236.3555 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 : 1.024 ------------------------------------------------------------------------------- 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: 5.9990 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 8988 Z= 0.368 Angle : 0.725 11.850 12186 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 *********************** 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 : 1.170 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: 1.3816 time to fit residues: 221.3245 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 : 1.002 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.111228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079610 restraints weight = 16261.421| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.28 r_work: 0.3036 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.206 Angle : 0.682 11.952 12186 Z= 0.341 Chirality : 0.048 0.544 1380 Planarity : 0.005 0.057 1541 Dihedral : 5.063 53.698 1237 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.29 % Allowed : 19.21 % 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: -0.32 (0.26), residues: 1105 helix: 1.48 (0.27), residues: 389 sheet: -0.74 (0.30), residues: 289 loop : -1.39 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 43 HIS 0.002 0.001 HIS A 329 PHE 0.011 0.001 PHE E 6 TYR 0.012 0.001 TYR A 65 ARG 0.010 0.000 ARG S 160 *********************** 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: 12 poor density : 148 time to evaluate : 1.058 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: 0.6907 (mmp) cc_final: 0.6451 (tpp) REVERT: A 295 HIS cc_start: 0.8408 (t70) cc_final: 0.8160 (t70) REVERT: C 313 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8797 (ptp-110) REVERT: B 19 ARG cc_start: 0.8324 (tmm160) cc_final: 0.8101 (tmm160) REVERT: B 130 GLU cc_start: 0.8594 (mp0) cc_final: 0.8375 (mp0) REVERT: B 215 GLU cc_start: 0.8733 (mp0) cc_final: 0.8492 (mp0) REVERT: B 259 GLN cc_start: 0.8487 (pt0) cc_final: 0.8219 (pt0) REVERT: B 262 MET cc_start: 0.8984 (mmt) cc_final: 0.8683 (tpp) REVERT: G 18 GLN cc_start: 0.7916 (tp40) cc_final: 0.7646 (tp40) REVERT: G 21 MET cc_start: 0.8941 (tmm) cc_final: 0.8709 (tmt) REVERT: G 22 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7761 (tm-30) REVERT: S 76 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8026 (pttm) REVERT: S 144 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7106 (p) outliers start: 12 outliers final: 6 residues processed: 155 average time/residue: 1.3402 time to fit residues: 220.2996 Evaluate side-chains 148 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 81 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9169 > 50: distance: 35 - 47: 17.051 distance: 43 - 47: 15.179 distance: 47 - 48: 23.372 distance: 48 - 49: 25.856 distance: 48 - 51: 22.301 distance: 49 - 50: 27.994 distance: 49 - 52: 24.370 distance: 52 - 53: 38.629 distance: 53 - 54: 7.100 distance: 53 - 56: 18.638 distance: 54 - 55: 22.779 distance: 54 - 60: 11.297 distance: 56 - 57: 13.727 distance: 57 - 58: 15.104 distance: 57 - 59: 14.638 distance: 60 - 61: 17.904 distance: 61 - 62: 8.250 distance: 61 - 64: 13.149 distance: 62 - 63: 29.128 distance: 62 - 70: 6.985 distance: 64 - 65: 17.761 distance: 65 - 66: 32.035 distance: 65 - 67: 10.723 distance: 66 - 68: 21.080 distance: 67 - 69: 20.781 distance: 68 - 69: 25.113 distance: 70 - 71: 22.761 distance: 71 - 72: 11.813 distance: 71 - 74: 15.993 distance: 72 - 73: 11.466 distance: 72 - 81: 26.578 distance: 74 - 75: 5.825 distance: 75 - 76: 15.801 distance: 76 - 77: 12.658 distance: 77 - 78: 5.961 distance: 78 - 79: 5.825 distance: 81 - 82: 20.525 distance: 82 - 83: 18.377 distance: 82 - 85: 8.527 distance: 83 - 84: 34.101 distance: 83 - 89: 10.267 distance: 85 - 86: 22.998 distance: 86 - 87: 30.940 distance: 86 - 88: 15.604 distance: 89 - 90: 8.871 distance: 90 - 91: 37.304 distance: 90 - 93: 23.787 distance: 91 - 92: 31.552 distance: 91 - 95: 44.510 distance: 93 - 94: 21.089 distance: 95 - 96: 37.145 distance: 95 - 101: 34.877 distance: 96 - 97: 11.973 distance: 96 - 99: 38.761 distance: 97 - 98: 15.448 distance: 97 - 102: 16.639 distance: 99 - 100: 34.513 distance: 100 - 101: 22.655 distance: 102 - 103: 34.316 distance: 103 - 104: 44.780 distance: 104 - 105: 43.172 distance: 104 - 106: 26.126 distance: 106 - 107: 29.264 distance: 106 - 112: 22.620 distance: 107 - 108: 30.670 distance: 107 - 110: 31.406 distance: 108 - 109: 38.337 distance: 108 - 113: 53.976 distance: 110 - 111: 43.421 distance: 111 - 112: 40.017 distance: 113 - 114: 26.644 distance: 114 - 115: 31.117 distance: 114 - 117: 19.480 distance: 115 - 116: 19.814 distance: 115 - 124: 22.352 distance: 117 - 118: 13.330 distance: 118 - 119: 19.746 distance: 119 - 120: 15.415 distance: 120 - 121: 14.587 distance: 121 - 122: 6.206 distance: 121 - 123: 18.773