Starting phenix.real_space_refine on Mon Nov 13 22:40:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/11_2023/7ji3_22343.pdb" } resolution = 3.46 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= -0.000 sd= 0.002 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 36 5.16 5 C 3837 2.51 5 N 1005 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6000 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 3.62, per 1000 atoms: 0.60 Number of scatterers: 6000 At special positions: 0 Unit cell: (84.7, 81.4, 127.6, 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 36 16.00 O 1122 8.00 N 1005 7.00 C 3837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 980.0 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 34.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 66 through 99 removed outlier: 3.755A pdb=" N ILE A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.524A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.946A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 332 removed outlier: 3.928A pdb=" N PHE A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 99 removed outlier: 3.755A pdb=" N ILE B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.525A pdb=" N ILE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.947A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 332 removed outlier: 3.927A pdb=" N PHE B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 99 removed outlier: 3.754A pdb=" N ILE C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.525A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.947A pdb=" N PHE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.928A pdb=" N PHE C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 13.982A pdb=" N TYR A 292 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 9.848A pdb=" N MET A 244 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN A 294 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 246 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A 296 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 248 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET A 298 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 243 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.336A pdb=" N GLN A 188 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS A 129 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 186 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS A 131 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET A 184 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 286 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A 238 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 283 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 156 removed outlier: 3.671A pdb=" N GLU A 155 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 108 removed outlier: 13.980A pdb=" N TYR B 292 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N MET B 244 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN B 294 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 246 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN B 296 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS B 248 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET B 298 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 132 removed outlier: 6.335A pdb=" N GLN B 188 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 129 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE B 186 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS B 131 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET B 184 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 286 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 238 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 283 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 156 removed outlier: 3.671A pdb=" N GLU B 155 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 119 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 108 removed outlier: 13.981A pdb=" N TYR C 292 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N MET C 244 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN C 294 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 246 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 296 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS C 248 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET C 298 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 243 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 132 removed outlier: 6.335A pdb=" N GLN C 188 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS C 129 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N PHE C 186 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS C 131 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET C 184 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 286 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 238 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 283 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 152 through 156 removed outlier: 3.672A pdb=" N GLU C 155 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 119 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 203 311 hydrogen bonds defined for protein. 861 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: 1.52 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1947 1.35 - 1.48: 1562 1.48 - 1.61: 2566 1.61 - 1.74: 0 1.74 - 1.86: 60 Bond restraints: 6135 Sorted by residual: bond pdb=" N ILE C 299 " pdb=" CA ILE C 299 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N ILE A 299 " pdb=" CA ILE A 299 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE B 299 " pdb=" CA ILE B 299 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C 308 " pdb=" CA ILE C 308 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N ILE B 308 " pdb=" CA ILE B 308 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.11e+00 ... (remaining 6130 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.45: 180 106.45 - 113.40: 3237 113.40 - 120.36: 2408 120.36 - 127.32: 2452 127.32 - 134.27: 54 Bond angle restraints: 8331 Sorted by residual: angle pdb=" N GLY B 223 " pdb=" CA GLY B 223 " pdb=" C GLY B 223 " ideal model delta sigma weight residual 112.50 107.99 4.51 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N GLY A 223 " pdb=" CA GLY A 223 " pdb=" C GLY A 223 " ideal model delta sigma weight residual 112.50 108.00 4.50 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N CYS C 225 " pdb=" CA CYS C 225 " pdb=" C CYS C 225 " ideal model delta sigma weight residual 112.54 116.65 -4.11 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N MET A 316 " pdb=" CA MET A 316 " pdb=" C MET A 316 " ideal model delta sigma weight residual 112.45 107.77 4.68 1.39e+00 5.18e-01 1.13e+01 angle pdb=" N CYS B 225 " pdb=" CA CYS B 225 " pdb=" C CYS B 225 " ideal model delta sigma weight residual 112.54 116.65 -4.11 1.22e+00 6.72e-01 1.13e+01 ... (remaining 8326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 3332 16.48 - 32.97: 266 32.97 - 49.45: 60 49.45 - 65.94: 7 65.94 - 82.42: 10 Dihedral angle restraints: 3675 sinusoidal: 1386 harmonic: 2289 Sorted by residual: dihedral pdb=" CB CYS C 225 " pdb=" SG CYS C 225 " pdb=" SG CYS C 229 " pdb=" CB CYS C 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.22 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS A 225 " pdb=" SG CYS A 225 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.22 37.22 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS B 225 " pdb=" SG CYS B 225 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.20 37.20 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 3672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 623 0.043 - 0.085: 182 0.085 - 0.127: 92 0.127 - 0.170: 28 0.170 - 0.212: 8 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA MET B 316 " pdb=" N MET B 316 " pdb=" C MET B 316 " pdb=" CB MET B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET A 316 " pdb=" N MET A 316 " pdb=" C MET A 316 " pdb=" CB MET A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA MET C 316 " pdb=" N MET C 316 " pdb=" C MET C 316 " pdb=" CB MET C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 930 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 142 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 143 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 142 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO C 143 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 142 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO B 143 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.037 5.00e-02 4.00e+02 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2164 2.87 - 3.38: 4914 3.38 - 3.89: 9427 3.89 - 4.39: 9936 4.39 - 4.90: 18361 Nonbonded interactions: 44802 Sorted by model distance: nonbonded pdb=" O PHE A 324 " pdb=" OG1 THR A 328 " model vdw 2.365 2.440 nonbonded pdb=" O PHE C 324 " pdb=" OG1 THR C 328 " model vdw 2.365 2.440 nonbonded pdb=" O PHE B 324 " pdb=" OG1 THR B 328 " model vdw 2.366 2.440 nonbonded pdb=" O PRO B 176 " pdb=" NE1 TRP B 288 " model vdw 2.416 2.520 nonbonded pdb=" O PRO A 176 " pdb=" NE1 TRP A 288 " model vdw 2.416 2.520 ... (remaining 44797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 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: 0.430 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: 2.450 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.080 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.005 0.056 6135 Z= 0.347 Angle : 0.793 6.426 8331 Z= 0.511 Chirality : 0.055 0.212 933 Planarity : 0.008 0.068 1077 Dihedral : 13.456 82.424 2172 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.13 (0.22), residues: 759 helix: -3.58 (0.21), residues: 255 sheet: -2.95 (0.22), residues: 312 loop : -2.99 (0.32), residues: 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2371 time to fit residues: 40.2050 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 99 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 188 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 280 GLN B 88 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 188 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 88 GLN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 188 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6135 Z= 0.256 Angle : 0.589 9.880 8331 Z= 0.294 Chirality : 0.042 0.189 933 Planarity : 0.006 0.052 1077 Dihedral : 4.540 22.996 831 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.24 % Allowed : 19.87 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.64 (0.27), residues: 759 helix: -0.36 (0.31), residues: 252 sheet: -2.08 (0.25), residues: 306 loop : -2.54 (0.37), residues: 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.2348 time to fit residues: 29.2810 Evaluate side-chains 82 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0554 time to fit residues: 1.6692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6135 Z= 0.224 Angle : 0.572 10.595 8331 Z= 0.280 Chirality : 0.041 0.139 933 Planarity : 0.004 0.043 1077 Dihedral : 4.286 21.750 831 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.80 % Allowed : 20.67 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.30), residues: 759 helix: 1.22 (0.33), residues: 252 sheet: -1.58 (0.27), residues: 306 loop : -2.26 (0.39), residues: 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 0.2267 time to fit residues: 23.6037 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0555 time to fit residues: 1.1413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6135 Z= 0.227 Angle : 0.600 11.241 8331 Z= 0.286 Chirality : 0.042 0.269 933 Planarity : 0.004 0.042 1077 Dihedral : 4.172 20.739 831 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.96 % Allowed : 19.87 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.31), residues: 759 helix: 1.76 (0.34), residues: 252 sheet: -1.25 (0.27), residues: 306 loop : -2.13 (0.40), residues: 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.808 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.2139 time to fit residues: 22.1894 Evaluate side-chains 74 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0556 time to fit residues: 1.4482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6135 Z= 0.247 Angle : 0.597 11.171 8331 Z= 0.285 Chirality : 0.041 0.134 933 Planarity : 0.004 0.043 1077 Dihedral : 4.130 21.171 831 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.80 % Allowed : 19.39 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.31), residues: 759 helix: 1.96 (0.33), residues: 252 sheet: -1.05 (0.27), residues: 306 loop : -2.05 (0.41), residues: 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.708 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.1935 time to fit residues: 19.6109 Evaluate side-chains 66 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0563 time to fit residues: 1.0203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.0000 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 188 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 287 GLN C 107 GLN C 287 GLN C 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6135 Z= 0.163 Angle : 0.598 12.114 8331 Z= 0.277 Chirality : 0.044 0.325 933 Planarity : 0.004 0.043 1077 Dihedral : 3.999 20.463 831 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.80 % Allowed : 21.15 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.31), residues: 759 helix: 2.05 (0.33), residues: 255 sheet: -0.81 (0.27), residues: 306 loop : -1.89 (0.43), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.666 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.1895 time to fit residues: 20.4142 Evaluate side-chains 71 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0564 time to fit residues: 1.3642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6135 Z= 0.371 Angle : 0.677 12.118 8331 Z= 0.327 Chirality : 0.044 0.289 933 Planarity : 0.004 0.043 1077 Dihedral : 4.321 20.546 831 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.64 % Allowed : 20.35 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.30), residues: 759 helix: 2.03 (0.33), residues: 255 sheet: -1.01 (0.27), residues: 300 loop : -1.80 (0.40), residues: 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.744 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1931 time to fit residues: 17.7243 Evaluate side-chains 67 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0597 time to fit residues: 1.2843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6135 Z= 0.315 Angle : 0.681 12.177 8331 Z= 0.322 Chirality : 0.045 0.355 933 Planarity : 0.004 0.045 1077 Dihedral : 4.305 20.411 831 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.80 % Allowed : 20.19 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.30), residues: 759 helix: 2.05 (0.33), residues: 255 sheet: -0.94 (0.27), residues: 300 loop : -1.75 (0.40), residues: 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.754 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1713 time to fit residues: 17.3334 Evaluate side-chains 69 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0531 time to fit residues: 1.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6135 Z= 0.282 Angle : 0.684 12.846 8331 Z= 0.320 Chirality : 0.045 0.359 933 Planarity : 0.004 0.044 1077 Dihedral : 4.291 20.697 831 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.80 % Allowed : 20.67 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.30), residues: 759 helix: 2.13 (0.33), residues: 255 sheet: -0.81 (0.28), residues: 300 loop : -1.73 (0.40), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.673 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1764 time to fit residues: 17.6554 Evaluate side-chains 69 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0568 time to fit residues: 1.2475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6135 Z= 0.328 Angle : 0.713 12.419 8331 Z= 0.337 Chirality : 0.045 0.347 933 Planarity : 0.004 0.045 1077 Dihedral : 4.398 20.057 831 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.48 % Allowed : 20.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.30), residues: 759 helix: 2.13 (0.32), residues: 255 sheet: -0.81 (0.28), residues: 300 loop : -1.76 (0.39), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.697 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 0.1736 time to fit residues: 16.7513 Evaluate side-chains 68 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0679 time to fit residues: 1.2677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3393 > 50: distance: 8 - 12: 3.960 distance: 12 - 13: 13.424 distance: 13 - 14: 14.204 distance: 13 - 16: 4.760 distance: 14 - 15: 15.659 distance: 14 - 19: 4.757 distance: 16 - 17: 13.803 distance: 16 - 18: 26.354 distance: 19 - 20: 8.699 distance: 19 - 180: 5.307 distance: 20 - 21: 13.980 distance: 20 - 23: 7.493 distance: 21 - 22: 6.321 distance: 21 - 26: 9.560 distance: 22 - 177: 6.341 distance: 23 - 24: 4.032 distance: 23 - 25: 4.709 distance: 26 - 27: 6.831 distance: 27 - 28: 4.763 distance: 27 - 30: 12.701 distance: 28 - 29: 7.843 distance: 28 - 38: 4.050 distance: 30 - 31: 8.140 distance: 31 - 32: 8.773 distance: 31 - 33: 5.637 distance: 32 - 34: 4.233 distance: 34 - 36: 6.958 distance: 35 - 36: 7.981 distance: 36 - 37: 5.338 distance: 38 - 39: 4.915 distance: 38 - 164: 4.019 distance: 39 - 40: 8.267 distance: 39 - 42: 5.659 distance: 40 - 41: 12.476 distance: 40 - 47: 9.321 distance: 41 - 161: 15.563 distance: 42 - 43: 16.774 distance: 43 - 44: 12.734 distance: 44 - 45: 9.654 distance: 44 - 46: 9.984 distance: 48 - 49: 8.965 distance: 48 - 51: 14.128 distance: 49 - 50: 12.851 distance: 49 - 56: 6.178 distance: 51 - 52: 21.777 distance: 52 - 53: 15.575 distance: 53 - 54: 14.097 distance: 53 - 55: 9.684 distance: 56 - 57: 11.589 distance: 57 - 58: 9.828 distance: 57 - 60: 16.722 distance: 58 - 59: 5.703 distance: 58 - 63: 7.287 distance: 60 - 61: 8.261 distance: 60 - 62: 11.026 distance: 63 - 64: 4.797 distance: 64 - 67: 5.622 distance: 65 - 66: 12.274 distance: 65 - 71: 5.989 distance: 67 - 68: 5.073 distance: 68 - 69: 6.757 distance: 68 - 70: 7.996 distance: 71 - 72: 7.437 distance: 72 - 73: 11.532 distance: 72 - 75: 6.310 distance: 73 - 74: 26.250 distance: 73 - 77: 27.129 distance: 75 - 76: 9.162 distance: 77 - 78: 24.848 distance: 78 - 79: 4.078 distance: 78 - 81: 20.047 distance: 79 - 80: 11.295 distance: 79 - 88: 6.908 distance: 81 - 82: 14.361 distance: 82 - 83: 10.732 distance: 82 - 84: 12.414 distance: 83 - 85: 15.622 distance: 84 - 86: 9.557 distance: 85 - 87: 13.103 distance: 86 - 87: 9.145 distance: 88 - 89: 6.353 distance: 88 - 94: 14.480 distance: 89 - 90: 3.950 distance: 89 - 92: 8.585 distance: 90 - 91: 19.439 distance: 90 - 95: 8.716 distance: 92 - 93: 19.254 distance: 93 - 94: 8.018