Starting phenix.real_space_refine on Tue Jun 10 11:30:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.map" model { file = "/net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7khf_22879/06_2025/7khf_22879.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7283 2.51 5 N 1924 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11559 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3250 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3253 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.44, per 1000 atoms: 0.64 Number of scatterers: 11559 At special positions: 0 Unit cell: (106.134, 137.541, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2314 8.00 N 1924 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 339 " - pdb=" SG CYS B 213 " distance=2.71 Simple disulfide: pdb=" SG CYS H 352 " - pdb=" SG CYS H 408 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 207 " " NAG E 1 " - " ASN H 186 " " NAG F 1 " - " ASN H 246 " " NAG G 1 " - " ASN A 186 " " NAG H 501 " - " ASN H 207 " " NAG I 1 " - " ASN A 246 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 31 sheets defined 15.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.814A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 69 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.749A pdb=" N TYR H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 197 " --> pdb=" O ARG H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 197' Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.632A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.050A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.562A pdb=" N LYS L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.044A pdb=" N GLY A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.035A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.596A pdb=" N HIS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.819A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.052A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.637A pdb=" N GLU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.018A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.256A pdb=" N ILE C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.551A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 303 removed outlier: 3.622A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.708A pdb=" N ARG H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.201A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY H 35 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 109 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 132 through 136 removed outlier: 4.049A pdb=" N GLN H 136 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 148 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 183 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU H 313 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 223 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H 198 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 161 " --> pdb=" O TYR H 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 172 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 175 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 276 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.107A pdb=" N VAL H 247 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 240 through 241 removed outlier: 3.752A pdb=" N TYR H 300 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 333 through 336 removed outlier: 3.686A pdb=" N GLY H 351 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP H 356 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 388 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER H 391 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 393 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR H 377 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 363 through 366 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.541A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.674A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.752A pdb=" N SER L 139 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR L 174 " --> pdb=" O ASP L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.554A pdb=" N LYS L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 97 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 115 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 99 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 113 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.926A pdb=" N THR A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.620A pdb=" N VAL A 161 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 159 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 172 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 235 removed outlier: 5.711A pdb=" N VAL A 247 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 284 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.711A pdb=" N SER A 325 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 300 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 274 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 155 through 156 436 hydrogen bonds defined for protein. 1086 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: 3.79 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1887 1.30 - 1.43: 3082 1.43 - 1.56: 6816 1.56 - 1.69: 0 1.69 - 1.82: 44 Bond restraints: 11829 Sorted by residual: bond pdb=" CA CYS H 352 " pdb=" C CYS H 352 " ideal model delta sigma weight residual 1.522 1.395 0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C PRO A 361 " pdb=" O PRO A 361 " ideal model delta sigma weight residual 1.235 1.178 0.057 7.90e-03 1.60e+04 5.16e+01 bond pdb=" C PRO A 359 " pdb=" O PRO A 359 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.10e-02 8.26e+03 3.39e+01 bond pdb=" N CYS H 352 " pdb=" CA CYS H 352 " ideal model delta sigma weight residual 1.454 1.386 0.069 1.27e-02 6.20e+03 2.92e+01 bond pdb=" CA SER H 389 " pdb=" CB SER H 389 " ideal model delta sigma weight residual 1.535 1.433 0.102 1.90e-02 2.77e+03 2.88e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15669 2.85 - 5.71: 402 5.71 - 8.56: 43 8.56 - 11.41: 10 11.41 - 14.26: 2 Bond angle restraints: 16126 Sorted by residual: angle pdb=" C PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 111.23 96.97 14.26 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C PRO A 361 " pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sigma weight residual 111.87 103.74 8.13 8.40e-01 1.42e+00 9.37e+01 angle pdb=" C THR A 372 " pdb=" CA THR A 372 " pdb=" CB THR A 372 " ideal model delta sigma weight residual 110.81 122.95 -12.14 1.73e+00 3.34e-01 4.93e+01 angle pdb=" CA PRO H 338 " pdb=" C PRO H 338 " pdb=" O PRO H 338 " ideal model delta sigma weight residual 119.34 109.12 10.22 1.47e+00 4.63e-01 4.84e+01 angle pdb=" C PRO H 335 " pdb=" CA PRO H 335 " pdb=" CB PRO H 335 " ideal model delta sigma weight residual 110.98 102.28 8.70 1.31e+00 5.83e-01 4.42e+01 ... (remaining 16121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6859 23.42 - 46.83: 347 46.83 - 70.25: 36 70.25 - 93.67: 10 93.67 - 117.09: 5 Dihedral angle restraints: 7257 sinusoidal: 2891 harmonic: 4366 Sorted by residual: dihedral pdb=" C PRO A 331 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta harmonic sigma weight residual -120.70 -102.15 -18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C PRO A 359 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " pdb=" CB PRO A 359 " ideal model delta harmonic sigma weight residual -120.70 -105.80 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 7254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1796 0.154 - 0.308: 58 0.308 - 0.462: 9 0.462 - 0.616: 0 0.616 - 0.770: 2 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA CYS H 352 " pdb=" N CYS H 352 " pdb=" C CYS H 352 " pdb=" CB CYS H 352 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 372 " pdb=" N THR A 372 " pdb=" C THR A 372 " pdb=" CB THR A 372 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1862 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 338 " 0.028 2.00e-02 2.50e+03 6.20e-02 3.84e+01 pdb=" C PRO H 338 " -0.107 2.00e-02 2.50e+03 pdb=" O PRO H 338 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS H 339 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " 0.001 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 246 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 335 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C PRO H 335 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO H 335 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 336 " -0.018 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 673 2.72 - 3.27: 11207 3.27 - 3.81: 16916 3.81 - 4.36: 19939 4.36 - 4.90: 36296 Nonbonded interactions: 85031 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" N GLY A 118 " model vdw 2.179 3.120 nonbonded pdb=" NZ LYS B 168 " pdb=" OD1 ASN B 172 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG H 68 " pdb=" OD2 ASP H 91 " model vdw 2.219 3.120 nonbonded pdb=" NZ LYS H 130 " pdb=" OG1 THR A 70 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU H 265 " pdb=" NH2 ARG H 301 " model vdw 2.318 3.120 ... (remaining 85026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 426 or resid 501)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.290 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.010 0.674 11854 Z= 0.556 Angle : 1.000 19.369 16186 Z= 0.630 Chirality : 0.069 0.770 1865 Planarity : 0.005 0.062 2064 Dihedral : 13.715 117.086 4424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 0.94 % Allowed : 1.57 % Favored : 97.49 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 3.85 % 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: -0.56 (0.23), residues: 1504 helix: 0.24 (0.40), residues: 178 sheet: 0.32 (0.23), residues: 553 loop : -1.03 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 256 HIS 0.005 0.001 HIS H 99 PHE 0.035 0.002 PHE A 358 TYR 0.040 0.002 TYR A 357 ARG 0.006 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 6) link_NAG-ASN : angle 4.03690 ( 18) link_BETA1-4 : bond 0.01065 ( 4) link_BETA1-4 : angle 2.62473 ( 12) hydrogen bonds : bond 0.26211 ( 414) hydrogen bonds : angle 9.30235 ( 1086) SS BOND : bond 0.17422 ( 15) SS BOND : angle 3.76488 ( 30) covalent geometry : bond 0.00772 (11829) covalent geometry : angle 0.97674 (16126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: H 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7637 (t-100) REVERT: H 257 MET cc_start: 0.7819 (mpp) cc_final: 0.7349 (mpp) REVERT: L 200 GLU cc_start: 0.7704 (pp20) cc_final: 0.7417 (pp20) REVERT: A 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 341 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5018 (tpp-160) REVERT: A 357 TYR cc_start: 0.8367 (p90) cc_final: 0.7530 (p90) REVERT: B 130 ASN cc_start: 0.8460 (m-40) cc_final: 0.7907 (t0) REVERT: D 288 GLN cc_start: 0.8515 (tp40) cc_final: 0.8274 (tp40) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8334 (tt) REVERT: C 230 THR cc_start: 0.9337 (m) cc_final: 0.9021 (p) REVERT: C 290 ASP cc_start: 0.7646 (m-30) cc_final: 0.7142 (m-30) outliers start: 12 outliers final: 4 residues processed: 186 average time/residue: 0.2201 time to fit residues: 59.1607 Evaluate side-chains 145 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082829 restraints weight = 22271.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086127 restraints weight = 11021.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088196 restraints weight = 7295.424| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11854 Z= 0.165 Angle : 0.670 8.641 16186 Z= 0.337 Chirality : 0.045 0.211 1865 Planarity : 0.005 0.038 2064 Dihedral : 9.276 103.578 1851 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.02 % Allowed : 8.07 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.50 (0.23), residues: 1504 helix: 0.08 (0.39), residues: 187 sheet: 0.41 (0.24), residues: 553 loop : -0.98 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 272 HIS 0.004 0.001 HIS L 199 PHE 0.027 0.001 PHE A 358 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.000 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 6) link_NAG-ASN : angle 2.44382 ( 18) link_BETA1-4 : bond 0.00742 ( 4) link_BETA1-4 : angle 2.87776 ( 12) hydrogen bonds : bond 0.04174 ( 414) hydrogen bonds : angle 6.49087 ( 1086) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.61082 ( 30) covalent geometry : bond 0.00386 (11829) covalent geometry : angle 0.66143 (16126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.260 Fit side-chains REVERT: H 256 TRP cc_start: 0.8120 (t60) cc_final: 0.7821 (t-100) REVERT: H 257 MET cc_start: 0.7974 (mpp) cc_final: 0.7746 (mpp) REVERT: H 353 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8005 (tp) REVERT: L 130 ASN cc_start: 0.8958 (t0) cc_final: 0.8689 (t0) REVERT: A 336 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 409 ASN cc_start: 0.8584 (m-40) cc_final: 0.8348 (m-40) REVERT: B 130 ASN cc_start: 0.8503 (m-40) cc_final: 0.7893 (t0) REVERT: B 140 ASP cc_start: 0.8290 (m-30) cc_final: 0.8080 (m-30) REVERT: B 168 LYS cc_start: 0.8434 (tptt) cc_final: 0.8032 (tptt) REVERT: D 279 ASP cc_start: 0.8225 (p0) cc_final: 0.7988 (p0) REVERT: D 288 GLN cc_start: 0.8243 (tp40) cc_final: 0.7924 (tp40) REVERT: C 219 ASP cc_start: 0.6934 (t70) cc_final: 0.6731 (t70) REVERT: C 290 ASP cc_start: 0.8101 (m-30) cc_final: 0.7328 (m-30) outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.2215 time to fit residues: 55.2797 Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 0.2980 chunk 82 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.081922 restraints weight = 22412.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085175 restraints weight = 11020.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087261 restraints weight = 7288.812| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11854 Z= 0.172 Angle : 0.637 8.964 16186 Z= 0.317 Chirality : 0.043 0.206 1865 Planarity : 0.004 0.036 2064 Dihedral : 8.842 100.514 1847 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.04 % Allowed : 10.10 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.47 (0.23), residues: 1504 helix: 0.16 (0.39), residues: 187 sheet: 0.35 (0.23), residues: 570 loop : -0.93 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 187 HIS 0.004 0.001 HIS H 99 PHE 0.027 0.001 PHE H 334 TYR 0.038 0.001 TYR A 357 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 6) link_NAG-ASN : angle 2.80636 ( 18) link_BETA1-4 : bond 0.00717 ( 4) link_BETA1-4 : angle 2.78823 ( 12) hydrogen bonds : bond 0.03844 ( 414) hydrogen bonds : angle 5.92760 ( 1086) SS BOND : bond 0.00349 ( 15) SS BOND : angle 0.67620 ( 30) covalent geometry : bond 0.00409 (11829) covalent geometry : angle 0.62644 (16126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 256 TRP cc_start: 0.8150 (t60) cc_final: 0.7551 (t-100) REVERT: H 257 MET cc_start: 0.7991 (mpp) cc_final: 0.7732 (mpp) REVERT: H 336 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (pp) REVERT: H 420 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: L 35 TYR cc_start: 0.9024 (m-80) cc_final: 0.8682 (m-80) REVERT: L 130 ASN cc_start: 0.9039 (t0) cc_final: 0.8725 (t0) REVERT: A 336 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8562 (pp) REVERT: A 409 ASN cc_start: 0.8652 (m-40) cc_final: 0.8334 (m-40) REVERT: B 78 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8347 (mp10) REVERT: B 130 ASN cc_start: 0.8539 (m-40) cc_final: 0.7909 (t0) REVERT: D 288 GLN cc_start: 0.8266 (tp40) cc_final: 0.7942 (tp40) REVERT: C 290 ASP cc_start: 0.8061 (m-30) cc_final: 0.7312 (m-30) outliers start: 26 outliers final: 21 residues processed: 167 average time/residue: 0.2155 time to fit residues: 52.8658 Evaluate side-chains 167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082618 restraints weight = 22973.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085723 restraints weight = 11588.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087746 restraints weight = 7765.798| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11854 Z= 0.275 Angle : 0.695 9.417 16186 Z= 0.347 Chirality : 0.045 0.215 1865 Planarity : 0.004 0.037 2064 Dihedral : 8.752 96.260 1847 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.82 % Allowed : 11.82 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.59 (0.22), residues: 1504 helix: 0.08 (0.39), residues: 187 sheet: 0.32 (0.23), residues: 574 loop : -1.08 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 49 HIS 0.006 0.001 HIS H 99 PHE 0.020 0.002 PHE H 334 TYR 0.025 0.002 TYR A 357 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 6) link_NAG-ASN : angle 2.91807 ( 18) link_BETA1-4 : bond 0.00671 ( 4) link_BETA1-4 : angle 2.73409 ( 12) hydrogen bonds : bond 0.04032 ( 414) hydrogen bonds : angle 5.82254 ( 1086) SS BOND : bond 0.00336 ( 15) SS BOND : angle 0.69177 ( 30) covalent geometry : bond 0.00657 (11829) covalent geometry : angle 0.68453 (16126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8728 (p0) cc_final: 0.8459 (p0) REVERT: H 336 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8870 (pp) REVERT: H 353 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (tp) REVERT: H 420 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: L 130 ASN cc_start: 0.9049 (t0) cc_final: 0.8752 (t0) REVERT: A 409 ASN cc_start: 0.8674 (m-40) cc_final: 0.8334 (m-40) REVERT: B 78 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8512 (mp10) REVERT: B 130 ASN cc_start: 0.8620 (m-40) cc_final: 0.7986 (t0) REVERT: B 168 LYS cc_start: 0.8483 (tppt) cc_final: 0.8152 (tptt) REVERT: D 279 ASP cc_start: 0.8263 (p0) cc_final: 0.8036 (p0) REVERT: D 288 GLN cc_start: 0.8414 (tp40) cc_final: 0.8084 (tp40) REVERT: C 290 ASP cc_start: 0.7918 (m-30) cc_final: 0.7217 (m-30) outliers start: 36 outliers final: 24 residues processed: 164 average time/residue: 0.2275 time to fit residues: 54.7668 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086132 restraints weight = 22655.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089345 restraints weight = 11331.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091419 restraints weight = 7555.618| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11854 Z= 0.132 Angle : 0.609 9.911 16186 Z= 0.299 Chirality : 0.043 0.210 1865 Planarity : 0.004 0.036 2064 Dihedral : 8.339 92.844 1847 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.19 % Allowed : 13.55 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.42 (0.23), residues: 1504 helix: 0.15 (0.39), residues: 187 sheet: 0.48 (0.23), residues: 571 loop : -0.98 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 256 HIS 0.004 0.001 HIS H 99 PHE 0.016 0.001 PHE H 334 TYR 0.023 0.001 TYR A 357 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 2.79458 ( 18) link_BETA1-4 : bond 0.00688 ( 4) link_BETA1-4 : angle 2.68404 ( 12) hydrogen bonds : bond 0.03189 ( 414) hydrogen bonds : angle 5.51147 ( 1086) SS BOND : bond 0.00251 ( 15) SS BOND : angle 0.50390 ( 30) covalent geometry : bond 0.00311 (11829) covalent geometry : angle 0.59781 (16126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8723 (p0) cc_final: 0.8312 (p0) REVERT: H 257 MET cc_start: 0.7832 (mpp) cc_final: 0.7139 (mpp) REVERT: H 336 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8706 (pp) REVERT: H 353 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7995 (tp) REVERT: H 420 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: L 35 TYR cc_start: 0.9013 (m-80) cc_final: 0.8793 (m-80) REVERT: L 130 ASN cc_start: 0.9064 (t0) cc_final: 0.8769 (t0) REVERT: A 409 ASN cc_start: 0.8698 (m-40) cc_final: 0.8359 (m-40) REVERT: B 78 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8275 (mp10) REVERT: B 130 ASN cc_start: 0.8602 (m-40) cc_final: 0.7953 (t0) REVERT: B 168 LYS cc_start: 0.8453 (tppt) cc_final: 0.8075 (tptt) REVERT: D 288 GLN cc_start: 0.8344 (tp40) cc_final: 0.8006 (tp40) REVERT: C 290 ASP cc_start: 0.7944 (m-30) cc_final: 0.7243 (m-30) outliers start: 28 outliers final: 18 residues processed: 165 average time/residue: 0.2108 time to fit residues: 51.4814 Evaluate side-chains 157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084495 restraints weight = 21234.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087566 restraints weight = 10606.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089554 restraints weight = 6968.305| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11854 Z= 0.135 Angle : 0.611 10.457 16186 Z= 0.299 Chirality : 0.043 0.228 1865 Planarity : 0.004 0.035 2064 Dihedral : 7.939 86.799 1845 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.58 % Allowed : 13.63 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.31 (0.23), residues: 1504 helix: 0.16 (0.39), residues: 187 sheet: 0.55 (0.23), residues: 567 loop : -0.88 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 PHE 0.013 0.001 PHE H 334 TYR 0.020 0.001 TYR A 357 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 2.78807 ( 18) link_BETA1-4 : bond 0.00724 ( 4) link_BETA1-4 : angle 2.66216 ( 12) hydrogen bonds : bond 0.03082 ( 414) hydrogen bonds : angle 5.36783 ( 1086) SS BOND : bond 0.00225 ( 15) SS BOND : angle 0.46838 ( 30) covalent geometry : bond 0.00321 (11829) covalent geometry : angle 0.60040 (16126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8747 (p0) cc_final: 0.8352 (p0) REVERT: H 257 MET cc_start: 0.7788 (mpp) cc_final: 0.7148 (mpp) REVERT: H 336 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (pp) REVERT: H 353 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (tp) REVERT: H 420 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: L 130 ASN cc_start: 0.8929 (t0) cc_final: 0.8658 (t0) REVERT: A 87 MET cc_start: 0.8304 (mmm) cc_final: 0.8069 (mmm) REVERT: A 409 ASN cc_start: 0.8662 (m-40) cc_final: 0.8320 (m-40) REVERT: B 78 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8395 (mp10) REVERT: B 130 ASN cc_start: 0.8600 (m-40) cc_final: 0.7996 (t0) REVERT: B 168 LYS cc_start: 0.8362 (tppt) cc_final: 0.8088 (tptt) REVERT: D 288 GLN cc_start: 0.8482 (tp40) cc_final: 0.8155 (tp40) REVERT: C 290 ASP cc_start: 0.7915 (m-30) cc_final: 0.7240 (m-30) outliers start: 33 outliers final: 26 residues processed: 161 average time/residue: 0.2420 time to fit residues: 58.3216 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 102 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084686 restraints weight = 21227.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087690 restraints weight = 10710.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089610 restraints weight = 7136.655| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11854 Z= 0.105 Angle : 0.589 11.186 16186 Z= 0.286 Chirality : 0.042 0.234 1865 Planarity : 0.004 0.033 2064 Dihedral : 7.438 76.790 1845 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.19 % Allowed : 14.33 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.20 (0.23), residues: 1504 helix: 0.24 (0.39), residues: 181 sheet: 0.62 (0.23), residues: 569 loop : -0.80 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 49 HIS 0.003 0.000 HIS H 99 PHE 0.012 0.001 PHE H 334 TYR 0.017 0.001 TYR C 223 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 2.79449 ( 18) link_BETA1-4 : bond 0.00739 ( 4) link_BETA1-4 : angle 2.65828 ( 12) hydrogen bonds : bond 0.02825 ( 414) hydrogen bonds : angle 5.21125 ( 1086) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.39950 ( 30) covalent geometry : bond 0.00245 (11829) covalent geometry : angle 0.57794 (16126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8759 (p0) cc_final: 0.8397 (p0) REVERT: H 257 MET cc_start: 0.7540 (mpp) cc_final: 0.7179 (mpp) REVERT: H 336 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8786 (pp) REVERT: H 353 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8298 (tp) REVERT: H 420 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: L 130 ASN cc_start: 0.8900 (t0) cc_final: 0.8622 (t0) REVERT: L 200 GLU cc_start: 0.7994 (pp20) cc_final: 0.7780 (pp20) REVERT: A 409 ASN cc_start: 0.8657 (m-40) cc_final: 0.8349 (m-40) REVERT: B 78 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8430 (mp10) REVERT: B 130 ASN cc_start: 0.8583 (m-40) cc_final: 0.7976 (t0) REVERT: B 168 LYS cc_start: 0.8312 (tppt) cc_final: 0.8032 (tptt) REVERT: D 288 GLN cc_start: 0.8486 (tp40) cc_final: 0.8164 (tp40) REVERT: C 219 ASP cc_start: 0.6197 (t70) cc_final: 0.5956 (t70) REVERT: C 231 THR cc_start: 0.8685 (p) cc_final: 0.8476 (t) REVERT: C 290 ASP cc_start: 0.7856 (m-30) cc_final: 0.7187 (m-30) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 0.2219 time to fit residues: 55.7544 Evaluate side-chains 162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.084083 restraints weight = 21189.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087115 restraints weight = 10785.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089040 restraints weight = 7142.878| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11854 Z= 0.120 Angle : 0.596 11.493 16186 Z= 0.288 Chirality : 0.042 0.235 1865 Planarity : 0.004 0.033 2064 Dihedral : 7.118 70.672 1843 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.51 % Allowed : 14.49 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.22 (0.22), residues: 1504 helix: 0.25 (0.39), residues: 183 sheet: 0.69 (0.23), residues: 562 loop : -0.88 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 49 HIS 0.003 0.001 HIS H 99 PHE 0.017 0.001 PHE H 287 TYR 0.017 0.001 TYR A 357 ARG 0.002 0.000 ARG L 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 6) link_NAG-ASN : angle 2.92510 ( 18) link_BETA1-4 : bond 0.00729 ( 4) link_BETA1-4 : angle 2.65893 ( 12) hydrogen bonds : bond 0.02843 ( 414) hydrogen bonds : angle 5.14260 ( 1086) SS BOND : bond 0.00208 ( 15) SS BOND : angle 0.43889 ( 30) covalent geometry : bond 0.00286 (11829) covalent geometry : angle 0.58454 (16126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8729 (p0) cc_final: 0.8368 (p0) REVERT: H 257 MET cc_start: 0.7549 (mpp) cc_final: 0.7180 (mpp) REVERT: H 336 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8828 (pp) REVERT: H 353 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8321 (tp) REVERT: H 420 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: L 130 ASN cc_start: 0.8892 (t0) cc_final: 0.8624 (t0) REVERT: A 409 ASN cc_start: 0.8659 (m-40) cc_final: 0.8320 (m-40) REVERT: B 78 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8447 (mp10) REVERT: B 130 ASN cc_start: 0.8593 (m-40) cc_final: 0.7980 (t0) REVERT: B 168 LYS cc_start: 0.8349 (tppt) cc_final: 0.8024 (tptt) REVERT: D 288 GLN cc_start: 0.8483 (tp40) cc_final: 0.8156 (tp40) REVERT: C 231 THR cc_start: 0.8741 (p) cc_final: 0.8537 (t) REVERT: C 290 ASP cc_start: 0.7883 (m-30) cc_final: 0.7200 (m-30) outliers start: 32 outliers final: 22 residues processed: 156 average time/residue: 0.2335 time to fit residues: 54.2332 Evaluate side-chains 153 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0763 > 50: distance: 17 - 101: 12.182 distance: 32 - 89: 31.258 distance: 35 - 86: 15.287 distance: 55 - 60: 3.645 distance: 60 - 61: 7.016 distance: 61 - 62: 12.403 distance: 62 - 63: 30.161 distance: 62 - 64: 25.512 distance: 64 - 65: 13.407 distance: 65 - 66: 19.298 distance: 65 - 68: 8.043 distance: 66 - 67: 22.102 distance: 66 - 73: 20.245 distance: 68 - 69: 16.444 distance: 69 - 70: 16.647 distance: 70 - 71: 21.354 distance: 70 - 72: 26.965 distance: 73 - 74: 9.987 distance: 74 - 75: 19.853 distance: 74 - 77: 15.153 distance: 75 - 76: 4.515 distance: 75 - 79: 5.743 distance: 77 - 78: 22.597 distance: 79 - 80: 5.806 distance: 79 - 85: 14.203 distance: 80 - 81: 20.968 distance: 80 - 83: 19.042 distance: 81 - 82: 11.347 distance: 81 - 86: 12.676 distance: 83 - 84: 17.070 distance: 84 - 85: 8.415 distance: 86 - 87: 4.559 distance: 87 - 88: 8.170 distance: 87 - 90: 18.691 distance: 88 - 89: 23.542 distance: 88 - 93: 11.313 distance: 90 - 92: 10.612 distance: 93 - 94: 6.555 distance: 94 - 95: 5.614 distance: 94 - 97: 7.246 distance: 95 - 96: 11.196 distance: 95 - 101: 5.187 distance: 97 - 98: 9.594 distance: 98 - 99: 6.943 distance: 98 - 100: 11.983 distance: 101 - 102: 6.803 distance: 102 - 105: 3.091 distance: 103 - 104: 8.221 distance: 103 - 109: 4.194 distance: 105 - 106: 13.131 distance: 106 - 107: 6.340 distance: 106 - 108: 6.011 distance: 109 - 110: 4.084 distance: 111 - 112: 14.062 distance: 111 - 117: 8.808 distance: 113 - 114: 8.376 distance: 113 - 115: 3.943 distance: 114 - 116: 6.832 distance: 117 - 118: 7.084 distance: 118 - 119: 6.486 distance: 118 - 121: 6.462 distance: 119 - 120: 21.174 distance: 119 - 129: 5.526 distance: 121 - 122: 3.016 distance: 122 - 123: 9.245 distance: 123 - 125: 6.004 distance: 125 - 127: 3.948 distance: 127 - 128: 5.403 distance: 129 - 130: 8.150 distance: 130 - 131: 4.210 distance: 130 - 133: 3.744 distance: 131 - 132: 12.850 distance: 131 - 138: 11.085 distance: 133 - 134: 6.803 distance: 134 - 135: 7.693 distance: 135 - 136: 12.426 distance: 136 - 137: 12.982