Starting phenix.real_space_refine on Sun Dec 10 16:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgs_31978/12_2023/7vgs_31978.pdb" } resolution = 2.8 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= 0.003 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5342 atoms to isotropic. 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 52 5.16 5 C 6208 2.51 5 N 1606 2.21 5 O 1834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 84": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1587 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "C" Number of atoms: 1683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1662 Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1587 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "E" Number of atoms: 1683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1662 Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 6.78, per 1000 atoms: 0.70 Number of scatterers: 9700 At special positions: 0 Unit cell: (73.455, 133.215, 141.93, 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 52 16.00 O 1834 8.00 N 1606 7.00 C 6208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS C 138 " - pdb=" SG ACYS C 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS C 138 " - pdb=" SG BCYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS E 138 " - pdb=" SG ACYS E 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS E 138 " - pdb=" SG BCYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " distance=2.04 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: 3.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 20 sheets defined 16.7% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 removed outlier: 3.631A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 106 removed outlier: 3.991A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 88 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP C 34 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.540A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 37 removed outlier: 4.426A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 78 through 106 removed outlier: 3.992A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP E 34 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.539A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.902A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.405A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER C 135 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 185 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 137 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 183 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 139 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER C 181 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 141 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET C 179 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.205A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.719A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 40 " --> pdb=" O ASN D 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.309A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D 170 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR D 176 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 168 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 178 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.903A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.406A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.100A pdb=" N SER E 135 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU E 185 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL E 137 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 183 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE E 139 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER E 181 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN E 141 " --> pdb=" O MET E 179 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET E 179 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.204A pdb=" N TRP E 152 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.720A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 40 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.308A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 170 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR F 176 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 168 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 178 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154 394 hydrogen bonds defined for protein. 1018 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: 2.75 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3042 1.35 - 1.46: 2479 1.46 - 1.58: 4357 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9952 Sorted by residual: bond pdb=" CA LYS A 162 " pdb=" CB LYS A 162 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.32e-02 5.74e+03 5.38e+00 bond pdb=" CA LYS B 162 " pdb=" CB LYS B 162 " ideal model delta sigma weight residual 1.522 1.553 -0.030 1.32e-02 5.74e+03 5.25e+00 bond pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB GLU B 18 " pdb=" CG GLU B 18 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C ASP E 98 " pdb=" N PRO E 99 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.20e-02 6.94e+03 1.39e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 327 106.87 - 113.66: 5523 113.66 - 120.44: 3558 120.44 - 127.22: 4055 127.22 - 134.01: 129 Bond angle restraints: 13592 Sorted by residual: angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" CA LEU B 90 " pdb=" CB LEU B 90 " pdb=" CG LEU B 90 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" N PHE B 45 " pdb=" CA PHE B 45 " pdb=" C PHE B 45 " ideal model delta sigma weight residual 113.61 109.94 3.67 1.50e+00 4.44e-01 6.00e+00 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 113.61 109.96 3.65 1.50e+00 4.44e-01 5.92e+00 angle pdb=" N SER C 7 " pdb=" CA SER C 7 " pdb=" C SER C 7 " ideal model delta sigma weight residual 109.81 115.12 -5.31 2.21e+00 2.05e-01 5.78e+00 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5490 17.93 - 35.85: 368 35.85 - 53.78: 44 53.78 - 71.71: 10 71.71 - 89.63: 8 Dihedral angle restraints: 5920 sinusoidal: 2228 harmonic: 3692 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 5917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1174 0.044 - 0.087: 274 0.087 - 0.131: 96 0.131 - 0.175: 12 0.175 - 0.218: 4 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA GLU A 18 " pdb=" N GLU A 18 " pdb=" C GLU A 18 " pdb=" CB GLU A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA GLU B 18 " pdb=" N GLU B 18 " pdb=" C GLU B 18 " pdb=" CB GLU B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE C 2 " pdb=" CA ILE C 2 " pdb=" CG1 ILE C 2 " pdb=" CG2 ILE C 2 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1557 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 165 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 164 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 165 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.031 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1405 2.76 - 3.30: 9273 3.30 - 3.83: 15939 3.83 - 4.37: 18389 4.37 - 4.90: 31637 Nonbonded interactions: 76643 Sorted by model distance: nonbonded pdb=" OG1 THR A 116 " pdb=" O LEU A 133 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR B 116 " pdb=" O LEU B 133 " model vdw 2.231 2.440 nonbonded pdb=" O ASN C 35 " pdb=" OG1 THR C 55 " model vdw 2.241 2.440 nonbonded pdb=" O ASN E 35 " pdb=" OG1 THR E 55 " model vdw 2.241 2.440 nonbonded pdb=" OG SER D 190 " pdb=" OE1 GLU D 191 " model vdw 2.246 2.440 ... (remaining 76638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 191 or resid 193 through 197 or resid 199 through 211 o \ r resid 213 through 218)) selection = (chain 'E' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 191 or resid 193 through 197 or resid 199 through 211 o \ r resid 213 through 218)) } ncs_group { reference = chain 'D' selection = chain 'F' } 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=0.27 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 3.490 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.450 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.002 0.042 9952 Z= 0.161 Angle : 0.660 8.959 13592 Z= 0.342 Chirality : 0.044 0.218 1560 Planarity : 0.005 0.056 1708 Dihedral : 12.190 89.633 3530 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.38 % Allowed : 0.56 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.16 (0.24), residues: 1254 helix: -0.43 (0.39), residues: 168 sheet: 0.18 (0.25), residues: 490 loop : -1.71 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.002 0.001 HIS D 41 PHE 0.008 0.001 PHE B 28 TYR 0.008 0.001 TYR C 53 ARG 0.001 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 1.0114 time to fit residues: 327.9905 Evaluate side-chains 186 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2285 time to fit residues: 1.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.0870 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN C 41 GLN C 42 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN D 39 GLN D 100 ASN E 41 GLN E 42 GLN E 128 GLN E 142 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN F 39 GLN F 100 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9952 Z= 0.293 Angle : 0.691 9.223 13592 Z= 0.351 Chirality : 0.046 0.176 1560 Planarity : 0.005 0.055 1708 Dihedral : 4.865 31.060 1378 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.90 % Allowed : 15.35 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.02 (0.24), residues: 1254 helix: 0.28 (0.38), residues: 184 sheet: 0.03 (0.24), residues: 516 loop : -1.69 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 152 HIS 0.005 0.001 HIS E 80 PHE 0.025 0.002 PHE A 45 TYR 0.024 0.002 TYR E 53 ARG 0.014 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 198 average time/residue: 1.1053 time to fit residues: 235.7094 Evaluate side-chains 187 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 7 average time/residue: 0.3976 time to fit residues: 4.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 0.0570 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 142 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9952 Z= 0.339 Angle : 0.702 8.416 13592 Z= 0.360 Chirality : 0.047 0.213 1560 Planarity : 0.005 0.057 1708 Dihedral : 5.218 36.866 1378 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.18 % Allowed : 17.61 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.22 (0.24), residues: 1254 helix: -0.07 (0.38), residues: 198 sheet: -0.18 (0.24), residues: 518 loop : -1.68 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 58 HIS 0.005 0.001 HIS A 148 PHE 0.020 0.002 PHE E 122 TYR 0.020 0.002 TYR E 36 ARG 0.004 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 171 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 198 average time/residue: 1.1053 time to fit residues: 236.1645 Evaluate side-chains 183 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.4910 time to fit residues: 6.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9952 Z= 0.271 Angle : 0.669 7.674 13592 Z= 0.344 Chirality : 0.045 0.204 1560 Planarity : 0.005 0.057 1708 Dihedral : 5.134 37.142 1378 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.90 % Allowed : 19.77 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.22 (0.24), residues: 1254 helix: -0.05 (0.37), residues: 198 sheet: -0.17 (0.24), residues: 518 loop : -1.70 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 58 HIS 0.004 0.001 HIS E 80 PHE 0.020 0.002 PHE A 45 TYR 0.020 0.002 TYR C 53 ARG 0.009 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 198 average time/residue: 1.0501 time to fit residues: 224.6886 Evaluate side-chains 179 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 20 residues processed: 9 average time/residue: 0.3514 time to fit residues: 5.2149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9952 Z= 0.378 Angle : 0.717 7.874 13592 Z= 0.368 Chirality : 0.047 0.235 1560 Planarity : 0.005 0.063 1708 Dihedral : 5.413 40.458 1378 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.59 % Allowed : 20.15 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.35 (0.24), residues: 1254 helix: -0.11 (0.37), residues: 200 sheet: -0.22 (0.24), residues: 520 loop : -1.86 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 58 HIS 0.005 0.002 HIS E 80 PHE 0.024 0.002 PHE B 193 TYR 0.023 0.002 TYR C 53 ARG 0.009 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 154 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 36 residues processed: 194 average time/residue: 1.0479 time to fit residues: 220.1338 Evaluate side-chains 182 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 26 residues processed: 10 average time/residue: 0.2412 time to fit residues: 4.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9952 Z= 0.253 Angle : 0.687 12.985 13592 Z= 0.347 Chirality : 0.045 0.206 1560 Planarity : 0.005 0.061 1708 Dihedral : 5.258 39.012 1378 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.37 % Allowed : 21.85 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.24 (0.24), residues: 1254 helix: 0.01 (0.37), residues: 198 sheet: -0.17 (0.24), residues: 508 loop : -1.74 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 58 HIS 0.003 0.001 HIS A 125 PHE 0.022 0.002 PHE A 45 TYR 0.019 0.002 TYR C 53 ARG 0.008 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 191 average time/residue: 1.0461 time to fit residues: 216.1906 Evaluate side-chains 181 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 9 average time/residue: 0.3044 time to fit residues: 4.9697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9952 Z= 0.218 Angle : 0.676 9.360 13592 Z= 0.340 Chirality : 0.044 0.193 1560 Planarity : 0.005 0.060 1708 Dihedral : 5.081 39.519 1378 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.80 % Allowed : 23.26 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.08 (0.25), residues: 1254 helix: 0.14 (0.37), residues: 196 sheet: -0.03 (0.24), residues: 514 loop : -1.69 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 58 HIS 0.003 0.001 HIS C 193 PHE 0.011 0.001 PHE C 122 TYR 0.018 0.001 TYR E 53 ARG 0.008 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 154 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 39 residues processed: 187 average time/residue: 1.0846 time to fit residues: 219.8598 Evaluate side-chains 187 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 29 residues processed: 10 average time/residue: 0.1318 time to fit residues: 3.4022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9952 Z= 0.194 Angle : 0.657 9.919 13592 Z= 0.330 Chirality : 0.044 0.181 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.976 37.528 1378 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.80 % Allowed : 23.35 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.01 (0.25), residues: 1254 helix: 0.19 (0.37), residues: 198 sheet: 0.03 (0.25), residues: 504 loop : -1.64 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 58 HIS 0.003 0.001 HIS C 193 PHE 0.019 0.001 PHE A 45 TYR 0.018 0.001 TYR E 53 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 150 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 183 average time/residue: 1.0228 time to fit residues: 202.8434 Evaluate side-chains 176 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 7 average time/residue: 0.1374 time to fit residues: 2.9554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.7980 chunk 102 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9952 Z= 0.195 Angle : 0.664 10.836 13592 Z= 0.332 Chirality : 0.044 0.185 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.917 38.179 1378 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.95 % Allowed : 23.63 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.89 (0.25), residues: 1254 helix: 0.22 (0.37), residues: 198 sheet: 0.11 (0.24), residues: 514 loop : -1.57 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 58 HIS 0.003 0.001 HIS C 193 PHE 0.015 0.001 PHE C 213 TYR 0.018 0.001 TYR E 53 ARG 0.011 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 31 residues processed: 178 average time/residue: 0.9943 time to fit residues: 192.7537 Evaluate side-chains 176 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.1488 time to fit residues: 3.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 53.161 > 50: distance: 55 - 57: 20.028 distance: 57 - 58: 16.251 distance: 58 - 59: 19.731 distance: 58 - 61: 12.734 distance: 59 - 60: 5.324 distance: 59 - 68: 13.081 distance: 61 - 62: 30.706 distance: 62 - 63: 14.200 distance: 63 - 64: 16.190 distance: 65 - 66: 12.258 distance: 65 - 67: 18.502 distance: 68 - 69: 26.381 distance: 69 - 70: 11.560 distance: 69 - 72: 7.182 distance: 70 - 71: 21.881 distance: 70 - 74: 12.782 distance: 72 - 73: 10.755 distance: 74 - 75: 18.612 distance: 75 - 76: 13.070 distance: 75 - 78: 11.811 distance: 76 - 77: 27.087 distance: 76 - 82: 19.886 distance: 78 - 79: 24.094 distance: 79 - 80: 24.126 distance: 79 - 81: 28.924 distance: 82 - 83: 12.791 distance: 83 - 84: 31.384 distance: 83 - 86: 11.271 distance: 84 - 85: 7.131 distance: 84 - 90: 10.938 distance: 86 - 87: 23.062 distance: 86 - 88: 28.794 distance: 87 - 89: 13.464 distance: 90 - 91: 29.379 distance: 91 - 92: 23.718 distance: 91 - 94: 34.025 distance: 92 - 93: 25.653 distance: 92 - 99: 29.786 distance: 94 - 95: 26.718 distance: 95 - 96: 10.986 distance: 96 - 97: 16.055 distance: 97 - 98: 10.337 distance: 99 - 100: 12.044 distance: 100 - 101: 13.562 distance: 100 - 103: 5.466 distance: 101 - 102: 32.450 distance: 101 - 107: 16.256 distance: 103 - 104: 20.482 distance: 104 - 106: 11.009 distance: 107 - 108: 25.224 distance: 108 - 109: 4.624 distance: 108 - 111: 33.246 distance: 109 - 110: 21.453 distance: 109 - 115: 22.026 distance: 111 - 112: 25.885 distance: 112 - 113: 26.083 distance: 112 - 114: 32.120 distance: 115 - 116: 7.608 distance: 115 - 121: 17.387 distance: 116 - 117: 8.773 distance: 116 - 119: 29.616 distance: 117 - 118: 9.217 distance: 119 - 120: 11.146 distance: 120 - 121: 21.523 distance: 122 - 123: 12.734 distance: 123 - 124: 10.903 distance: 123 - 126: 31.850 distance: 124 - 131: 9.703 distance: 126 - 127: 24.015 distance: 127 - 128: 14.605 distance: 128 - 129: 19.156 distance: 129 - 130: 22.267 distance: 131 - 132: 3.486 distance: 131 - 161: 17.652 distance: 132 - 133: 23.521 distance: 132 - 135: 30.468 distance: 133 - 140: 7.403 distance: 134 - 158: 7.484 distance: 135 - 136: 23.593 distance: 136 - 137: 13.336 distance: 137 - 138: 15.848 distance: 137 - 139: 15.813