Starting phenix.real_space_refine on Sat Jan 20 12:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/01_2024/7uze_26886_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/01_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_26886/01_2024/7uze_26886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/01_2024/7uze_26886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/01_2024/7uze_26886_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/01_2024/7uze_26886_trim_updated.pdb" } 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 7392 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-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 14969 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 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, 3661 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: 3670 Chain: "B" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 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, 3661 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: 3670 Chain: "C" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 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, 3661 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: 3670 Chain: "A" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 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, 3661 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: 3670 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: 13.02, per 1000 atoms: 0.87 Number of scatterers: 14969 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 7392 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: 13.95 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 49 through 71 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 77 through 86 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 135 through 156 Processing helix chain 'D' and resid 168 through 187 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 193 through 203 removed outlier: 3.699A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 229 removed outlier: 5.576A pdb=" N GLY D 215 " --> pdb=" O PHE D 212 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.675A pdb=" N ASP D 228 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 229 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 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 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 71 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 77 through 86 Processing helix chain 'B' and resid 91 through 115 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 168 through 187 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 193 through 203 removed outlier: 3.694A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 229 removed outlier: 5.554A pdb=" N GLY B 215 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 3.674A pdb=" N ASP B 228 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 229 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 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 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 49 through 71 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 77 through 86 Processing helix chain 'C' and resid 91 through 115 Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 168 through 187 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 193 through 202 removed outlier: 3.707A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 229 removed outlier: 5.561A pdb=" N GLY C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.675A pdb=" N ASP C 228 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE C 229 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 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 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 49 through 71 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 77 through 86 Processing helix chain 'A' and resid 91 through 115 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 168 through 187 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 193 through 203 removed outlier: 3.690A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 229 removed outlier: 5.559A pdb=" N GLY A 215 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.669A pdb=" N ASP A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 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) 467 hydrogen bonds defined for protein. 1257 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: 5.50 Time building geometry restraints manager: 14.41 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: 26 1.23 - 1.42: 3074 1.42 - 1.62: 4504 1.62 - 1.81: 28 Bond restraints: 15012 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 15007 not shown) Histogram of bond angle deviations from ideal: 101.51 - 108.00: 2536 108.00 - 114.49: 15911 114.49 - 120.99: 5474 120.99 - 127.48: 3031 127.48 - 133.97: 76 Bond angle restraints: 27028 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 27023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6471 17.97 - 35.94: 432 35.94 - 53.91: 113 53.91 - 71.88: 12 71.88 - 89.85: 12 Dihedral angle restraints: 7040 sinusoidal: 3784 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 7037 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: 1910 2.25 - 2.84: 34396 2.84 - 3.42: 43628 3.42 - 4.01: 60426 4.01 - 4.60: 91675 Nonbonded interactions: 232035 Sorted by model distance: nonbonded pdb=" HH TYR D 186 " pdb=" O GLY C 30 " model vdw 1.661 1.850 nonbonded pdb=" HH TYR C 186 " pdb=" O GLY A 30 " model vdw 1.664 1.850 nonbonded pdb=" O VAL D 244 " pdb=" H GLY D 248 " model vdw 1.667 1.850 nonbonded pdb=" O GLY D 30 " pdb=" HH TYR B 186 " model vdw 1.671 1.850 nonbonded pdb=" O GLY B 30 " pdb=" HH TYR A 186 " model vdw 1.674 1.850 ... (remaining 232030 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' 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: 0.730 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: 0.260 Extract box with map and model: 3.820 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 61.910 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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= 0.210 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 : 1.275 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 2.2580 time to fit residues: 183.7934 Evaluate side-chains 73 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN A 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0410 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= 0.311 Angle : 0.608 7.349 10392 Z= 0.329 Chirality : 0.040 0.161 1268 Planarity : 0.005 0.034 1272 Dihedral : 9.362 59.512 1376 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer: Outliers : 2.30 % Allowed : 13.11 % 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: 1.00 (0.26), residues: 980 helix: 1.27 (0.18), residues: 640 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 213 HIS 0.005 0.002 HIS A 69 PHE 0.021 0.002 PHE A 212 TYR 0.011 0.002 TYR D 227 ARG 0.002 0.000 ARG D 195 *********************** 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 91 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.159 Fit side-chains REVERT: D 191 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8134 (mp) REVERT: D 225 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8219 (tm) REVERT: B 36 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8679 (mttm) REVERT: B 225 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8226 (tm) REVERT: C 225 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8172 (tm) REVERT: A 225 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8119 (tm) outliers start: 17 outliers final: 4 residues processed: 87 average time/residue: 2.0675 time to fit residues: 193.5212 Evaluate side-chains 77 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 225 LEU 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: 0.0030 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.0349 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= 0.178 Angle : 0.524 7.268 10392 Z= 0.282 Chirality : 0.037 0.150 1268 Planarity : 0.004 0.032 1272 Dihedral : 7.848 47.786 1376 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer: Outliers : 1.89 % Allowed : 13.38 % Favored : 84.73 % 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: 1.22 (0.26), residues: 980 helix: 1.50 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 11 HIS 0.004 0.001 HIS B 180 PHE 0.015 0.001 PHE B 212 TYR 0.009 0.001 TYR D 227 ARG 0.001 0.000 ARG B 195 *********************** 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 90 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7972 (mp) REVERT: D 225 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8174 (tm) REVERT: B 225 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8177 (tm) REVERT: C 225 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8133 (tm) REVERT: A 225 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8075 (tm) outliers start: 14 outliers final: 5 residues processed: 87 average time/residue: 2.2026 time to fit residues: 205.5641 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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: 0.0429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7620 Z= 0.251 Angle : 0.559 7.342 10392 Z= 0.300 Chirality : 0.038 0.157 1268 Planarity : 0.004 0.033 1272 Dihedral : 8.415 50.167 1372 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer: Outliers : 1.49 % Allowed : 13.78 % Favored : 84.73 % 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: 0.97 (0.26), residues: 980 helix: 1.29 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 340 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 A 212 TYR 0.010 0.002 TYR D 227 ARG 0.001 0.000 ARG D 195 *********************** 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 88 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8073 (mp) REVERT: D 225 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8182 (tm) REVERT: B 225 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8189 (tm) REVERT: C 225 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 225 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8100 (tm) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 2.1903 time to fit residues: 202.2798 Evaluate side-chains 80 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- 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: 0.8705 moved from start: 0.0469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.252 Angle : 0.562 7.340 10392 Z= 0.301 Chirality : 0.038 0.158 1268 Planarity : 0.004 0.034 1272 Dihedral : 8.532 52.170 1372 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 13.24 % 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: 0.90 (0.26), residues: 980 helix: 1.24 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 340 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 0.017 0.002 PHE B 212 TYR 0.010 0.002 TYR D 227 ARG 0.001 0.000 ARG B 195 *********************** 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 90 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8097 (mp) REVERT: D 225 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8179 (tm) REVERT: B 225 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8195 (tm) REVERT: C 225 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8136 (tm) REVERT: A 225 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8092 (tm) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 2.1672 time to fit residues: 200.4149 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7620 Z= 0.199 Angle : 0.533 7.284 10392 Z= 0.285 Chirality : 0.037 0.153 1268 Planarity : 0.004 0.033 1272 Dihedral : 7.896 50.571 1372 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer: Outliers : 1.89 % Allowed : 13.51 % 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: 1.05 (0.26), residues: 980 helix: 1.36 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 213 HIS 0.004 0.001 HIS B 180 PHE 0.015 0.002 PHE B 212 TYR 0.009 0.002 TYR D 227 ARG 0.001 0.000 ARG B 195 *********************** 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 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8031 (mp) REVERT: D 225 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8172 (tm) REVERT: B 225 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8180 (tm) REVERT: C 225 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8119 (tm) REVERT: A 225 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8090 (tm) outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 2.2019 time to fit residues: 198.5669 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7620 Z= 0.217 Angle : 0.539 7.269 10392 Z= 0.288 Chirality : 0.037 0.154 1268 Planarity : 0.004 0.034 1272 Dihedral : 7.980 50.371 1372 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 13.24 % 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: 0.98 (0.26), residues: 980 helix: 1.30 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 213 HIS 0.005 0.001 HIS D 180 PHE 0.016 0.002 PHE B 212 TYR 0.009 0.002 TYR D 227 ARG 0.001 0.000 ARG B 195 *********************** 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 88 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 191 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8029 (mp) REVERT: D 225 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8174 (tm) REVERT: B 225 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8182 (tm) REVERT: C 225 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8123 (tm) REVERT: A 225 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8085 (tm) outliers start: 16 outliers final: 8 residues processed: 84 average time/residue: 2.1488 time to fit residues: 193.8741 Evaluate side-chains 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 69.9732 > 50: distance: 3 - 36: 25.851 distance: 27 - 36: 26.173 distance: 36 - 37: 9.725 distance: 36 - 41: 22.371 distance: 37 - 38: 20.972 distance: 37 - 40: 27.352 distance: 37 - 42: 32.787 distance: 38 - 39: 25.056 distance: 38 - 46: 37.853 distance: 40 - 43: 20.351 distance: 40 - 44: 28.234 distance: 40 - 45: 24.327 distance: 46 - 47: 22.170 distance: 46 - 54: 18.739 distance: 47 - 48: 17.693 distance: 47 - 50: 18.155 distance: 47 - 55: 26.895 distance: 48 - 49: 25.976 distance: 48 - 65: 35.286 distance: 50 - 51: 23.062 distance: 50 - 56: 18.167 distance: 50 - 57: 20.558 distance: 51 - 52: 9.478 distance: 51 - 53: 9.266 distance: 51 - 58: 13.227 distance: 52 - 59: 3.546 distance: 53 - 62: 7.466 distance: 53 - 64: 6.831 distance: 65 - 66: 13.260 distance: 65 - 69: 18.065 distance: 66 - 67: 27.500 distance: 66 - 70: 9.913 distance: 66 - 71: 20.217 distance: 67 - 68: 36.906 distance: 67 - 72: 34.382 distance: 72 - 73: 20.596 distance: 72 - 83: 4.260 distance: 73 - 74: 18.106 distance: 73 - 76: 27.078 distance: 73 - 84: 32.516 distance: 74 - 75: 5.998 distance: 74 - 92: 28.624 distance: 76 - 77: 37.540 distance: 76 - 85: 23.154 distance: 76 - 86: 28.243 distance: 77 - 78: 19.659 distance: 77 - 79: 19.801 distance: 78 - 80: 15.303 distance: 78 - 87: 15.292 distance: 79 - 81: 20.699 distance: 79 - 88: 17.250 distance: 80 - 82: 6.419 distance: 80 - 89: 5.688 distance: 81 - 82: 5.196 distance: 81 - 90: 4.644 distance: 82 - 91: 4.753 distance: 92 - 93: 42.406 distance: 92 - 101: 48.879 distance: 93 - 94: 54.225 distance: 93 - 96: 13.548 distance: 93 - 102: 14.089 distance: 94 - 95: 14.959 distance: 94 - 114: 47.700 distance: 96 - 97: 7.722 distance: 96 - 103: 16.866 distance: 96 - 104: 18.096 distance: 97 - 98: 23.274 distance: 97 - 105: 33.163 distance: 97 - 106: 37.859 distance: 98 - 99: 22.647 distance: 98 - 107: 16.853 distance: 98 - 108: 14.642 distance: 99 - 100: 11.360 distance: 99 - 109: 9.335 distance: 99 - 110: 9.183 distance: 100 - 111: 6.548 distance: 100 - 112: 6.137 distance: 100 - 113: 4.794 distance: 114 - 115: 40.258 distance: 115 - 116: 69.969 distance: 115 - 118: 55.974 distance: 115 - 127: 39.349 distance: 116 - 117: 39.744 distance: 116 - 135: 9.761 distance: 118 - 119: 39.966 distance: 118 - 128: 11.523 distance: 119 - 120: 44.192 distance: 119 - 121: 15.354 distance: 120 - 122: 10.570 distance: 120 - 130: 30.252 distance: 121 - 123: 24.801 distance: 121 - 131: 13.476 distance: 122 - 124: 10.743 distance: 122 - 132: 13.350 distance: 123 - 124: 13.933 distance: 123 - 133: 10.477 distance: 124 - 125: 17.497 distance: 125 - 134: 25.353 distance: 135 - 136: 42.042 distance: 135 - 141: 4.155 distance: 136 - 137: 19.897 distance: 136 - 139: 8.874 distance: 136 - 142: 31.312 distance: 137 - 138: 18.830 distance: 137 - 149: 12.378 distance: 139 - 140: 34.936 distance: 139 - 143: 17.682 distance: 139 - 144: 31.428 distance: 140 - 141: 35.313 distance: 140 - 145: 15.159 distance: 140 - 146: 26.902 distance: 141 - 147: 18.364 distance: 141 - 148: 32.429 distance: 149 - 150: 42.657 distance: 149 - 156: 50.553 distance: 150 - 151: 15.742 distance: 150 - 157: 13.486 distance: 151 - 152: 17.786 distance: 151 - 165: 22.764 distance: 153 - 154: 9.760 distance: 153 - 155: 13.551 distance: 153 - 158: 18.296 distance: 154 - 159: 18.665 distance: 154 - 160: 19.621 distance: 154 - 161: 19.478 distance: 155 - 162: 11.605 distance: 155 - 163: 15.176 distance: 155 - 164: 18.254 distance: 165 - 166: 53.124 distance: 165 - 169: 21.575 distance: 166 - 167: 10.770 distance: 166 - 170: 5.856 distance: 166 - 171: 26.432 distance: 167 - 168: 8.153 distance: 167 - 172: 50.635 distance: 172 - 173: 40.741 distance: 172 - 180: 40.031 distance: 173 - 174: 28.684 distance: 173 - 176: 5.005 distance: 173 - 181: 15.619 distance: 174 - 175: 11.980 distance: 174 - 186: 22.933 distance: 176 - 177: 36.131 distance: 176 - 182: 17.474 distance: 176 - 183: 26.155 distance: 177 - 178: 20.155 distance: 177 - 179: 23.941 distance: 179 - 184: 19.211 distance: 179 - 185: 19.411