Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:16:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/12_2022/7uze_26886_trim_updated_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/12_2022/7uze_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_26886/12_2022/7uze_26886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/12_2022/7uze_26886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/12_2022/7uze_26886_trim_updated_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/12_2022/7uze_26886_trim_updated_trim_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ASP 163": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 13.06, 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: 14.46 Conformation dependent library (CDL) restraints added in 2.4 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: 0.66 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: 5.34 Time building geometry restraints manager: 14.97 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: 5413 17.97 - 35.94: 400 35.94 - 53.91: 91 53.91 - 71.88: 12 71.88 - 89.85: 12 Dihedral angle restraints: 5928 sinusoidal: 2672 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 5925 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 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. 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: 0.500 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: 0.250 Extract box with map and model: 4.060 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.110 Process input model: 59.580 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 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 : 15.317 89.846 2592 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer Outliers : 0.68 % 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 *********************** 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 : 1.186 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 1.9272 time to fit residues: 158.5560 Evaluate side-chains 73 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 7620 Z= 0.215 Angle : 0.556 7.249 10392 Z= 0.300 Chirality : 0.037 0.153 1268 Planarity : 0.005 0.031 1272 Dihedral : 7.603 43.226 1148 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer Outliers : 2.43 % 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: 1.30 (0.26), residues: 980 helix: 1.51 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 336 *********************** 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 93 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.239 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 88 average time/residue: 1.7316 time to fit residues: 166.2482 Evaluate side-chains 84 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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: 0.8753 moved from start: 0.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 7620 Z= 0.238 Angle : 0.567 7.482 10392 Z= 0.302 Chirality : 0.038 0.160 1268 Planarity : 0.004 0.032 1272 Dihedral : 7.917 48.469 1148 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer Outliers : 1.22 % 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: 1.06 (0.26), residues: 980 helix: 1.36 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 340 *********************** 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: 9 poor density : 81 time to evaluate : 1.126 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 1.7156 time to fit residues: 165.7919 Evaluate side-chains 79 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.2932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.8777 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7620 Z= 0.358 Angle : 0.631 7.316 10392 Z= 0.337 Chirality : 0.041 0.166 1268 Planarity : 0.005 0.033 1272 Dihedral : 9.511 57.628 1148 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer Outliers : 2.30 % 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: 0.70 (0.25), residues: 980 helix: 1.07 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 344 *********************** 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 85 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 82 average time/residue: 1.5832 time to fit residues: 141.8871 Evaluate side-chains 67 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.3472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.0445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 7620 Z= 0.210 Angle : 0.550 7.416 10392 Z= 0.293 Chirality : 0.037 0.157 1268 Planarity : 0.004 0.032 1272 Dihedral : 9.029 59.175 1148 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer Outliers : 2.30 % 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: 0.94 (0.26), residues: 980 helix: 1.27 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 340 *********************** 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 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 1.7868 time to fit residues: 175.4048 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.0470 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= 0.222 Angle : 0.558 7.284 10392 Z= 0.295 Chirality : 0.037 0.156 1268 Planarity : 0.004 0.032 1272 Dihedral : 8.634 57.575 1148 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.41 % Favored : 96.18 % Rotamer Outliers : 1.35 % 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: 0.96 (0.26), residues: 980 helix: 1.29 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 340 *********************** 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: 10 poor density : 77 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 87 average time/residue: 1.7752 time to fit residues: 168.2316 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.8733 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 7620 Z= 0.160 Angle : 0.514 7.258 10392 Z= 0.272 Chirality : 0.036 0.149 1268 Planarity : 0.004 0.031 1272 Dihedral : 7.270 53.579 1148 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer Outliers : 2.16 % 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: 1.25 (0.26), residues: 980 helix: 1.53 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 340 *********************** 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 96 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 1.6823 time to fit residues: 172.8463 Evaluate side-chains 89 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.4479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 71.9719 > 50: distance: 3 - 36: 35.214 distance: 27 - 36: 35.536 distance: 36 - 41: 39.776 distance: 37 - 38: 56.741 distance: 37 - 40: 40.387 distance: 37 - 42: 56.266 distance: 38 - 39: 56.134 distance: 38 - 46: 54.654 distance: 40 - 43: 56.166 distance: 40 - 44: 40.344 distance: 40 - 45: 60.248 distance: 46 - 47: 57.817 distance: 46 - 54: 67.364 distance: 47 - 48: 35.734 distance: 47 - 50: 20.243 distance: 47 - 55: 25.774 distance: 48 - 49: 47.868 distance: 48 - 65: 64.020 distance: 50 - 51: 42.934 distance: 50 - 56: 51.826 distance: 50 - 57: 58.780 distance: 51 - 52: 22.071 distance: 51 - 53: 32.303 distance: 51 - 58: 32.519 distance: 52 - 59: 18.447 distance: 52 - 60: 31.043 distance: 52 - 61: 23.122 distance: 53 - 62: 41.617 distance: 53 - 63: 30.380 distance: 53 - 64: 26.384 distance: 65 - 66: 40.239 distance: 65 - 69: 56.985 distance: 66 - 67: 68.758 distance: 66 - 70: 39.869 distance: 66 - 71: 39.625 distance: 67 - 68: 56.916 distance: 67 - 72: 38.913 distance: 72 - 73: 57.323 distance: 72 - 83: 40.780 distance: 73 - 74: 39.769 distance: 73 - 76: 55.782 distance: 73 - 84: 40.030 distance: 74 - 92: 57.547 distance: 76 - 77: 70.717 distance: 76 - 85: 58.202 distance: 76 - 86: 68.683 distance: 77 - 78: 25.598 distance: 77 - 79: 38.341 distance: 78 - 80: 33.991 distance: 78 - 87: 43.297 distance: 79 - 81: 43.338 distance: 79 - 88: 43.438 distance: 80 - 82: 43.499 distance: 80 - 89: 39.215 distance: 81 - 82: 30.699 distance: 81 - 90: 24.138 distance: 82 - 91: 37.155 distance: 92 - 93: 57.266 distance: 92 - 101: 61.816 distance: 93 - 94: 39.194 distance: 93 - 96: 40.013 distance: 93 - 102: 55.726 distance: 94 - 95: 57.001 distance: 96 - 103: 40.183 distance: 97 - 98: 55.249 distance: 97 - 105: 69.311 distance: 97 - 106: 69.472 distance: 98 - 99: 42.632 distance: 98 - 107: 44.231 distance: 98 - 108: 50.778 distance: 99 - 100: 44.766 distance: 99 - 109: 44.362 distance: 99 - 110: 46.226 distance: 100 - 111: 38.533 distance: 100 - 112: 38.569 distance: 100 - 113: 45.645 distance: 114 - 115: 40.298 distance: 114 - 126: 56.977 distance: 115 - 116: 55.883 distance: 115 - 118: 69.003 distance: 115 - 127: 70.123 distance: 116 - 117: 40.303 distance: 118 - 119: 40.107 distance: 118 - 128: 11.846 distance: 118 - 129: 19.640 distance: 119 - 120: 68.768 distance: 119 - 121: 39.362 distance: 120 - 122: 41.581 distance: 120 - 130: 41.312 distance: 121 - 123: 39.056 distance: 121 - 131: 40.157 distance: 122 - 124: 47.834 distance: 122 - 132: 61.355 distance: 123 - 124: 47.276 distance: 123 - 133: 36.032 distance: 124 - 125: 26.232 distance: 125 - 134: 36.234 distance: 135 - 136: 55.879 distance: 135 - 141: 13.022 distance: 136 - 142: 25.626 distance: 137 - 138: 41.050 distance: 139 - 140: 56.771 distance: 139 - 143: 49.878 distance: 139 - 144: 39.133 distance: 140 - 141: 46.999 distance: 140 - 145: 57.665 distance: 140 - 146: 55.806 distance: 141 - 147: 12.979 distance: 141 - 148: 48.538 distance: 149 - 150: 69.795 distance: 149 - 156: 69.014 distance: 150 - 151: 46.843 distance: 151 - 152: 48.167 distance: 151 - 165: 39.268 distance: 153 - 158: 42.042 distance: 154 - 159: 68.547 distance: 154 - 160: 70.074 distance: 154 - 161: 60.341 distance: 155 - 162: 60.683 distance: 155 - 163: 60.095 distance: 155 - 164: 63.534 distance: 165 - 166: 44.749 distance: 165 - 169: 46.028 distance: 166 - 167: 69.471 distance: 166 - 171: 56.239 distance: 167 - 168: 70.060 distance: 167 - 172: 39.128 distance: 172 - 173: 39.297 distance: 172 - 180: 39.975 distance: 173 - 174: 40.261 distance: 173 - 181: 39.420 distance: 174 - 175: 37.550 distance: 174 - 186: 33.848 distance: 176 - 177: 39.457 distance: 176 - 182: 40.341 distance: 176 - 183: 43.716 distance: 177 - 178: 39.551 distance: 177 - 179: 40.640 distance: 179 - 184: 56.133 distance: 179 - 185: 66.269