Starting phenix.real_space_refine on Tue Aug 6 01:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/08_2024/7uze_26886_trim.cif" } resolution = 2.4 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= 0.006 sd= 0.357 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1409 1.98 5 H 7528 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 163": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15105 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "B" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "C" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "A" Number of atoms: 3720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3695 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3704 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (46 atoms not shown) pdb="HH22BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG A 234 " occ=0.49 Time building chain proxies: 13.05, per 1000 atoms: 0.86 Number of scatterers: 15105 At special positions: 0 Unit cell: (70.55, 90.885, 90.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1409 8.00 N 1264 7.00 C 4884 6.00 H 7528 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.06 Conformation dependent library (CDL) restraints added in 3.2 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 7 through 33 removed outlier: 3.508A pdb=" N TRP D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 48 through 72 removed outlier: 5.737A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 90 through 116 Processing helix chain 'D' and resid 134 through 157 Processing helix chain 'D' and resid 167 through 188 removed outlier: 5.628A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 removed outlier: 3.699A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.611A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 6 Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.509A pdb=" N TRP B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 48 through 72 removed outlier: 5.686A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 90 through 116 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 167 through 188 removed outlier: 5.611A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.694A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.610A pdb=" N LYS B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.514A pdb=" N TRP C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 48 through 72 removed outlier: 5.736A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 90 through 116 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 167 through 188 removed outlier: 5.633A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.707A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 230 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.626A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.509A pdb=" N TRP A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 48 through 72 removed outlier: 5.726A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 90 through 116 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 167 through 188 removed outlier: 5.618A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.690A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.612A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1596 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: 5.47 Time building geometry restraints manager: 14.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7380 1.03 - 1.23: 162 1.23 - 1.42: 3074 1.42 - 1.62: 4504 1.62 - 1.81: 28 Bond restraints: 15148 Sorted by residual: bond pdb=" CA CYS C 189 " pdb=" C CYS C 189 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.68e+00 bond pdb=" CA CYS A 189 " pdb=" C CYS A 189 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.52e+00 bond pdb=" CA CYS B 189 " pdb=" C CYS B 189 " ideal model delta sigma weight residual 1.532 1.521 0.011 9.60e-03 1.09e+04 1.37e+00 bond pdb=" CG PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.60e-01 bond pdb=" CA ILE D 191 " pdb=" CB ILE D 191 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.21e-01 ... (remaining 15143 not shown) Histogram of bond angle deviations from ideal: 101.51 - 108.00: 2610 108.00 - 114.49: 16173 114.49 - 120.99: 5474 120.99 - 127.48: 3031 127.48 - 133.97: 76 Bond angle restraints: 27364 Sorted by residual: angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 107.07 7.33 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N GLY D 190 " pdb=" CA GLY D 190 " pdb=" C GLY D 190 " ideal model delta sigma weight residual 113.18 107.15 6.03 2.37e+00 1.78e-01 6.47e+00 angle pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 114.17 117.70 -3.53 1.45e+00 4.76e-01 5.92e+00 angle pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N GLY B 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.70e+00 angle pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N GLY C 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.68e+00 ... (remaining 27359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 6836 26.78 - 53.56: 346 53.56 - 80.35: 79 80.35 - 107.13: 7 107.13 - 133.91: 4 Dihedral angle restraints: 7272 sinusoidal: 4016 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N ALA C 183 " pdb=" CA ALA C 183 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 828 0.031 - 0.061: 313 0.061 - 0.092: 101 0.092 - 0.123: 21 0.123 - 0.153: 5 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL D 133 " pdb=" N VAL D 133 " pdb=" C VAL D 133 " pdb=" CB VAL D 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1265 not shown) Planarity restraints: 2236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 191 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ILE A 191 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 191 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN A 192 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 76 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 77 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 225 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C LEU C 225 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU C 225 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 226 " 0.007 2.00e-02 2.50e+03 ... (remaining 2233 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1833 2.25 - 2.84: 34939 2.84 - 3.42: 44117 3.42 - 4.01: 61072 4.01 - 4.60: 92691 Nonbonded interactions: 234652 Sorted by model distance: nonbonded pdb=" HH TYR D 186 " pdb=" O GLY C 30 " model vdw 1.661 2.450 nonbonded pdb=" HH TYR C 186 " pdb=" O GLY A 30 " model vdw 1.664 2.450 nonbonded pdb=" O GLY D 30 " pdb=" HH TYR B 186 " model vdw 1.671 2.450 nonbonded pdb=" O GLY B 30 " pdb=" HH TYR A 186 " model vdw 1.674 2.450 nonbonded pdb=" HE ARG B 195 " pdb=" O HOH B 406 " model vdw 1.742 2.450 ... (remaining 234647 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'B' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'C' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'D' and (resid 3 through 233 or resid 236 through 249 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=0.99 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: 1.600 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: 0.270 Extract box with map and model: 1.120 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 61.530 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.003 0.022 7620 Z= 0.206 Angle : 0.584 7.334 10392 Z= 0.313 Chirality : 0.037 0.153 1268 Planarity : 0.003 0.029 1272 Dihedral : 14.965 89.846 2816 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 0.68 % Allowed : 14.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 980 helix: 1.85 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 11 HIS 0.004 0.001 HIS B 180 PHE 0.018 0.002 PHE D 212 TYR 0.010 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.310 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 2.3022 time to fit residues: 188.3059 Evaluate side-chains 72 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7620 Z= 0.201 Angle : 0.549 7.352 10392 Z= 0.296 Chirality : 0.038 0.150 1268 Planarity : 0.004 0.031 1272 Dihedral : 8.155 52.305 1376 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.10 % Favored : 96.49 % Rotamer: Outliers : 2.43 % Allowed : 12.97 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 980 helix: 2.05 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 11 HIS 0.004 0.001 HIS A 69 PHE 0.017 0.002 PHE A 212 TYR 0.010 0.002 TYR D 227 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 225 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8094 (tm) REVERT: B 36 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: B 225 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8110 (tm) REVERT: C 225 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8031 (tm) outliers start: 18 outliers final: 8 residues processed: 92 average time/residue: 2.2472 time to fit residues: 222.0593 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7620 Z= 0.309 Angle : 0.600 7.318 10392 Z= 0.325 Chirality : 0.040 0.158 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.791 52.172 1376 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer: Outliers : 2.30 % Allowed : 12.70 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 980 helix: 1.82 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 245 HIS 0.005 0.002 HIS A 69 PHE 0.020 0.002 PHE B 212 TYR 0.011 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 225 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8120 (tm) REVERT: B 36 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (mttm) REVERT: B 225 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8138 (tm) REVERT: C 225 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8075 (tm) REVERT: A 51 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8270 (tttt) REVERT: A 225 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8022 (tm) outliers start: 17 outliers final: 8 residues processed: 87 average time/residue: 2.3114 time to fit residues: 215.5288 Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7620 Z= 0.301 Angle : 0.597 7.352 10392 Z= 0.323 Chirality : 0.040 0.157 1268 Planarity : 0.004 0.033 1272 Dihedral : 8.793 54.324 1375 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 2.16 % Allowed : 12.97 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 980 helix: 1.73 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 245 HIS 0.005 0.002 HIS A 69 PHE 0.019 0.002 PHE B 212 TYR 0.011 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.231 Fit side-chains REVERT: D 191 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (mp) REVERT: D 225 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8115 (tm) REVERT: B 36 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8667 (mttm) REVERT: B 225 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8137 (tm) REVERT: C 51 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8255 (tttt) REVERT: C 225 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8080 (tm) REVERT: A 51 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8276 (tttt) REVERT: A 225 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8030 (tm) outliers start: 16 outliers final: 5 residues processed: 85 average time/residue: 2.2434 time to fit residues: 204.3301 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7620 Z= 0.217 Angle : 0.550 7.374 10392 Z= 0.297 Chirality : 0.037 0.151 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.269 52.257 1372 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 1.76 % Allowed : 13.92 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.27), residues: 980 helix: 2.00 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 213 HIS 0.004 0.001 HIS C 180 PHE 0.015 0.002 PHE A 212 TYR 0.009 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8042 (mp) REVERT: D 225 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8062 (tm) REVERT: B 36 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8665 (mttm) REVERT: B 225 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8091 (tm) REVERT: C 225 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8032 (tm) REVERT: A 225 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7979 (tm) outliers start: 13 outliers final: 5 residues processed: 85 average time/residue: 2.3403 time to fit residues: 214.9209 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7620 Z= 0.263 Angle : 0.575 7.348 10392 Z= 0.311 Chirality : 0.038 0.155 1268 Planarity : 0.004 0.033 1272 Dihedral : 8.507 54.752 1372 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.82 % Favored : 95.76 % Rotamer: Outliers : 2.30 % Allowed : 12.57 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 980 helix: 1.86 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 213 HIS 0.005 0.001 HIS D 180 PHE 0.018 0.002 PHE B 212 TYR 0.010 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.005 Fit side-chains REVERT: D 191 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8123 (mp) REVERT: D 225 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8095 (tm) REVERT: B 36 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8669 (mttm) REVERT: B 225 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8118 (tm) REVERT: C 51 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8212 (tttt) REVERT: C 225 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8060 (tm) REVERT: A 225 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8007 (tm) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 2.1832 time to fit residues: 201.9677 Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7620 Z= 0.312 Angle : 0.604 7.348 10392 Z= 0.327 Chirality : 0.040 0.158 1268 Planarity : 0.004 0.034 1272 Dihedral : 8.799 58.095 1372 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 2.16 % Allowed : 12.70 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 980 helix: 1.71 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 213 HIS 0.006 0.002 HIS D 180 PHE 0.019 0.002 PHE A 212 TYR 0.011 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8182 (mp) REVERT: D 225 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8123 (tm) REVERT: B 225 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8142 (tm) REVERT: C 225 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8089 (tm) REVERT: A 225 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8038 (tm) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 2.1055 time to fit residues: 188.2801 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4984 > 50: distance: 3 - 36: 10.553 distance: 8 - 46: 11.246 distance: 27 - 36: 9.563 distance: 36 - 37: 10.315 distance: 36 - 41: 11.020 distance: 37 - 38: 6.584 distance: 37 - 40: 6.223 distance: 37 - 42: 6.500 distance: 38 - 39: 19.424 distance: 38 - 46: 14.223 distance: 40 - 43: 6.566 distance: 40 - 44: 4.978 distance: 40 - 45: 5.187 distance: 46 - 47: 6.678 distance: 46 - 54: 14.621 distance: 47 - 48: 8.975 distance: 47 - 50: 7.188 distance: 47 - 55: 10.343 distance: 48 - 49: 5.977 distance: 48 - 65: 13.364 distance: 50 - 51: 5.426 distance: 50 - 56: 3.067 distance: 50 - 57: 4.825 distance: 51 - 52: 3.671 distance: 51 - 58: 4.060 distance: 65 - 69: 3.457 distance: 66 - 67: 12.795 distance: 66 - 70: 4.960 distance: 66 - 71: 6.784 distance: 67 - 68: 13.851 distance: 67 - 72: 10.293 distance: 68 - 114: 5.538 distance: 72 - 73: 19.229 distance: 72 - 83: 20.008 distance: 73 - 74: 27.484 distance: 73 - 76: 15.792 distance: 73 - 84: 19.486 distance: 74 - 75: 21.136 distance: 74 - 92: 20.772 distance: 76 - 77: 8.954 distance: 76 - 85: 6.888 distance: 76 - 86: 8.820 distance: 77 - 78: 3.378 distance: 77 - 79: 4.546 distance: 79 - 88: 3.014 distance: 92 - 93: 15.217 distance: 92 - 101: 12.657 distance: 93 - 94: 8.079 distance: 93 - 96: 20.256 distance: 93 - 102: 25.612 distance: 94 - 95: 32.096 distance: 94 - 114: 10.652 distance: 96 - 97: 14.339 distance: 96 - 103: 12.868 distance: 96 - 104: 13.905 distance: 97 - 98: 9.518 distance: 97 - 105: 14.773 distance: 97 - 106: 11.390 distance: 98 - 99: 3.892 distance: 98 - 107: 3.051 distance: 98 - 108: 8.883 distance: 99 - 100: 3.491 distance: 99 - 109: 3.381 distance: 99 - 110: 3.460 distance: 114 - 115: 29.835 distance: 114 - 126: 22.851 distance: 115 - 116: 35.604 distance: 115 - 118: 32.200 distance: 115 - 127: 23.577 distance: 116 - 117: 14.879 distance: 116 - 135: 9.998 distance: 118 - 119: 11.639 distance: 118 - 128: 5.145 distance: 118 - 129: 22.023 distance: 119 - 120: 8.657 distance: 120 - 122: 5.777 distance: 120 - 130: 4.702 distance: 121 - 123: 5.557 distance: 121 - 131: 4.575 distance: 122 - 124: 4.873 distance: 122 - 132: 3.817 distance: 123 - 124: 4.262 distance: 123 - 133: 3.330 distance: 124 - 125: 4.413 distance: 125 - 134: 6.742 distance: 135 - 136: 5.176 distance: 135 - 141: 12.755 distance: 136 - 137: 21.273 distance: 136 - 139: 11.716 distance: 136 - 142: 14.358 distance: 137 - 138: 22.536 distance: 137 - 149: 16.807 distance: 139 - 140: 11.830 distance: 139 - 143: 6.926 distance: 139 - 144: 7.661 distance: 140 - 141: 5.261 distance: 140 - 145: 9.832 distance: 140 - 146: 9.827 distance: 141 - 148: 7.956 distance: 149 - 150: 12.711 distance: 149 - 156: 16.231 distance: 150 - 151: 24.105 distance: 150 - 153: 8.871 distance: 150 - 157: 3.049 distance: 151 - 152: 20.612 distance: 151 - 165: 24.670 distance: 153 - 155: 3.352 distance: 153 - 158: 3.155 distance: 154 - 159: 6.175 distance: 154 - 161: 3.142 distance: 155 - 162: 4.413 distance: 165 - 166: 31.450 distance: 165 - 169: 19.103 distance: 166 - 167: 15.751 distance: 166 - 170: 16.124 distance: 166 - 171: 4.200 distance: 167 - 168: 13.584 distance: 167 - 172: 22.131 distance: 172 - 173: 6.233 distance: 172 - 180: 16.172 distance: 173 - 174: 8.911 distance: 173 - 181: 15.904 distance: 174 - 175: 5.650 distance: 174 - 186: 7.946 distance: 176 - 177: 13.085 distance: 176 - 182: 7.518 distance: 176 - 183: 6.789 distance: 177 - 178: 6.386 distance: 177 - 179: 7.815 distance: 179 - 184: 9.073 distance: 179 - 185: 12.031