Starting phenix.real_space_refine on Wed Apr 30 20:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.map" model { file = "/net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ito_60873/04_2025/9ito_60873.cif" } resolution = 3.3 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= -0.001 sd= 0.011 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 32 5.16 5 C 6648 2.51 5 N 1605 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9987 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "I" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Z" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2028 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 1 Chain: "Y" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 423 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "V" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 179 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 33} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "U" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 190 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 71 Chain: "T" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1630 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 74 Time building chain proxies: 7.13, per 1000 atoms: 0.71 Number of scatterers: 9987 At special positions: 0 Unit cell: (106.95, 106.95, 93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1702 8.00 N 1605 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.69 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 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 85.1% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.539A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 removed outlier: 4.444A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.529A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 38 removed outlier: 3.535A pdb=" N VAL I 22 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 removed outlier: 4.562A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 4.192A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 71 removed outlier: 3.900A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE J 55 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 removed outlier: 3.885A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 38 Processing helix chain 'K' and resid 41 through 72 removed outlier: 4.183A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 66 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 18 through 38 removed outlier: 4.065A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.082A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.504A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 3.521A pdb=" N VAL M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 71 removed outlier: 3.509A pdb=" N THR M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 5.198A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 4.300A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.715A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 42 through 72 removed outlier: 4.659A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.739A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 38 Processing helix chain 'P' and resid 41 through 72 removed outlier: 5.071A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA P 54 " --> pdb=" O PHE P 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.760A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 38 removed outlier: 4.094A pdb=" N VAL Q 22 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 72 removed outlier: 3.845A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 79 through 97 Processing helix chain 'Z' and resid 102 through 124 Proline residue: Z 108 - end of helix removed outlier: 3.611A pdb=" N THR Z 112 " --> pdb=" O PRO Z 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Z 119 " --> pdb=" O LEU Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 176 Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 211 removed outlier: 3.625A pdb=" N PHE Z 195 " --> pdb=" O LEU Z 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Z 196 " --> pdb=" O ASN Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 267 removed outlier: 3.847A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 4.022A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.592A pdb=" N ALA Z 292 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 29 Processing helix chain 'Y' and resid 29 through 56 Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 50 removed outlier: 3.550A pdb=" N ASP V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 40 removed outlier: 4.572A pdb=" N ARG X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Proline residue: X 32 - end of helix Processing helix chain 'U' and resid 9 through 45 removed outlier: 3.879A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.768A pdb=" N GLU U 45 " --> pdb=" O THR U 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.915A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.823A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.876A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 175 removed outlier: 4.561A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.955A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 210 removed outlier: 3.605A pdb=" N ALA T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 217 Processing helix chain 'T' and resid 228 through 268 removed outlier: 4.008A pdb=" N PHE T 236 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE T 237 " --> pdb=" O ILE T 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER T 238 " --> pdb=" O ILE T 234 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.679A pdb=" N GLY T 278 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE T 279 " --> pdb=" O PRO T 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 133 through 134 876 hydrogen bonds defined for protein. 2604 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: 3.17 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3172 1.34 - 1.46: 2228 1.46 - 1.58: 4704 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10164 Sorted by residual: bond pdb=" N ILE Z 39 " pdb=" CA ILE Z 39 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ILE I 70 " pdb=" CA ILE I 70 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.29e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.22e-02 6.72e+03 8.22e+00 bond pdb=" N ILE H 70 " pdb=" CA ILE H 70 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N VAL T 231 " pdb=" CA VAL T 231 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.97e+00 ... (remaining 10159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 13330 1.39 - 2.78: 395 2.78 - 4.17: 78 4.17 - 5.56: 28 5.56 - 6.95: 2 Bond angle restraints: 13833 Sorted by residual: angle pdb=" N VAL N 22 " pdb=" CA VAL N 22 " pdb=" C VAL N 22 " ideal model delta sigma weight residual 112.96 108.02 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N ILE P 70 " pdb=" CA ILE P 70 " pdb=" C ILE P 70 " ideal model delta sigma weight residual 111.67 107.08 4.59 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C CYS T 135 " pdb=" CA CYS T 135 " pdb=" CB CYS T 135 " ideal model delta sigma weight residual 111.86 106.55 5.31 1.34e+00 5.57e-01 1.57e+01 angle pdb=" N ILE Q 70 " pdb=" CA ILE Q 70 " pdb=" C ILE Q 70 " ideal model delta sigma weight residual 110.72 106.75 3.97 1.01e+00 9.80e-01 1.55e+01 angle pdb=" C ASP Z 41 " pdb=" CA ASP Z 41 " pdb=" CB ASP Z 41 " ideal model delta sigma weight residual 116.63 112.11 4.52 1.16e+00 7.43e-01 1.52e+01 ... (remaining 13828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 5045 17.35 - 34.69: 576 34.69 - 52.04: 162 52.04 - 69.38: 27 69.38 - 86.73: 11 Dihedral angle restraints: 5821 sinusoidal: 1996 harmonic: 3825 Sorted by residual: dihedral pdb=" CB CYS Z 135 " pdb=" SG CYS Z 135 " pdb=" SG CYS Z 173 " pdb=" CB CYS Z 173 " ideal model delta sinusoidal sigma weight residual 93.00 147.08 -54.08 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA MET Z 264 " pdb=" C MET Z 264 " pdb=" N ALA Z 265 " pdb=" CA ALA Z 265 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ARG H 44 " pdb=" C ARG H 44 " pdb=" N VAL H 45 " pdb=" CA VAL H 45 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1300 0.047 - 0.093: 336 0.093 - 0.140: 57 0.140 - 0.187: 14 0.187 - 0.233: 9 Chirality restraints: 1716 Sorted by residual: chirality pdb=" CA ILE M 70 " pdb=" N ILE M 70 " pdb=" C ILE M 70 " pdb=" CB ILE M 70 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE O 70 " pdb=" N ILE O 70 " pdb=" C ILE O 70 " pdb=" CB ILE O 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1713 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY O 19 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO O 20 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO L 20 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 19 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO J 20 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO J 20 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 20 " -0.034 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2506 2.79 - 3.32: 10665 3.32 - 3.85: 17494 3.85 - 4.37: 18894 4.37 - 4.90: 32880 Nonbonded interactions: 82439 Sorted by model distance: nonbonded pdb=" OD1 ASN V 7 " pdb=" OG1 THR V 9 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU H 42 " pdb=" OH TYR Q 48 " model vdw 2.294 3.040 nonbonded pdb=" O GLU T 235 " pdb=" OG SER T 238 " model vdw 2.298 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.318 3.040 nonbonded pdb=" O ARG T 249 " pdb=" ND2 ASN T 253 " model vdw 2.325 3.120 ... (remaining 82434 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = (chain 'T' and (resid 47 through 135 or resid 170 through 304)) selection = (chain 'Z' and ((resid 47 through 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 66 or (resid 67 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 120 or (resid 121 thro \ ugh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 or \ (resid 125 through 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 or (resid 129 and (name N or name CA or name C or name O or name C \ B )) or resid 130 or (resid 131 through 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 or (resid 134 and (name N or name CA or name C \ or name O or name CB )) or resid 135 or resid 170 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 182 o \ r (resid 183 through 189 and (name N or name CA or name C or name O or name CB ) \ ) or resid 190 through 217 or (resid 218 through 225 and (name N or name CA or n \ ame C or name O or name CB )) or resid 226 or (resid 227 through 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 304)) } ncs_group { reference = (chain 'U' and resid 8 through 40) selection = (chain 'X' and resid 8 through 40) } ncs_group { reference = (chain 'V' and resid 7 through 50) selection = (chain 'Y' and resid 7 through 50) } 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: 152.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.650 Find NCS groups from input model: 0.420 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.008 0.661 10165 Z= 0.409 Angle : 0.695 41.274 13835 Z= 0.415 Chirality : 0.045 0.233 1716 Planarity : 0.005 0.070 1745 Dihedral : 16.525 86.729 3378 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.95 % Allowed : 30.17 % Favored : 68.88 % 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: 0.55 (0.23), residues: 1342 helix: 0.92 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -2.42 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 170 PHE 0.026 0.001 PHE Z 276 TYR 0.013 0.001 TYR V 30 ARG 0.002 0.000 ARG Y 40 Details of bonding type rmsd hydrogen bonds : bond 0.14185 ( 876) hydrogen bonds : angle 6.16134 ( 2604) SS BOND : bond 0.66080 ( 1) SS BOND : angle 29.25561 ( 2) covalent geometry : bond 0.00448 (10164) covalent geometry : angle 0.59998 (13833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 325 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ILE cc_start: 0.9101 (tp) cc_final: 0.8788 (tp) REVERT: H 51 ILE cc_start: 0.9566 (pt) cc_final: 0.9346 (pt) REVERT: I 2 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8235 (mm-30) REVERT: I 5 ASN cc_start: 0.8688 (p0) cc_final: 0.8483 (p0) REVERT: I 38 ASN cc_start: 0.9028 (t0) cc_final: 0.8716 (t0) REVERT: I 40 GLU cc_start: 0.8662 (tp30) cc_final: 0.8295 (tp30) REVERT: I 48 TYR cc_start: 0.9176 (m-80) cc_final: 0.8956 (m-80) REVERT: J 38 ASN cc_start: 0.9256 (t0) cc_final: 0.9051 (t0) REVERT: K 1 MET cc_start: 0.6821 (mpt) cc_final: 0.5842 (mpt) REVERT: K 41 ILE cc_start: 0.9541 (tp) cc_final: 0.9304 (tp) REVERT: L 1 MET cc_start: 0.7649 (mtp) cc_final: 0.7329 (mtm) REVERT: N 41 ILE cc_start: 0.9175 (tp) cc_final: 0.8866 (tp) REVERT: P 4 LEU cc_start: 0.9374 (tp) cc_final: 0.9135 (tp) REVERT: P 42 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8567 (tm-30) REVERT: Z 23 PHE cc_start: 0.7247 (m-80) cc_final: 0.7015 (m-80) REVERT: Z 71 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7572 (ttm-80) REVERT: Z 239 GLU cc_start: 0.9273 (tp30) cc_final: 0.8561 (tp30) REVERT: Z 242 LYS cc_start: 0.9259 (tttt) cc_final: 0.8745 (mttm) REVERT: Y 31 ARG cc_start: 0.9010 (tpp-160) cc_final: 0.8568 (tpp80) REVERT: Y 34 MET cc_start: 0.8891 (mmp) cc_final: 0.8575 (tpp) REVERT: T 246 LEU cc_start: 0.9252 (mt) cc_final: 0.9023 (mt) REVERT: T 254 ILE cc_start: 0.9036 (mm) cc_final: 0.8440 (tt) REVERT: T 264 MET cc_start: 0.4659 (tpp) cc_final: 0.4288 (tpp) REVERT: T 291 PHE cc_start: 0.9115 (t80) cc_final: 0.8798 (t80) outliers start: 9 outliers final: 4 residues processed: 329 average time/residue: 0.2173 time to fit residues: 100.2378 Evaluate side-chains 275 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain T residue 135 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.123685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087736 restraints weight = 19289.643| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.90 r_work: 0.3139 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10165 Z= 0.149 Angle : 0.529 8.020 13835 Z= 0.282 Chirality : 0.041 0.185 1716 Planarity : 0.005 0.066 1745 Dihedral : 3.958 35.552 1435 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.64 % Allowed : 29.22 % Favored : 66.14 % 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: 1.41 (0.23), residues: 1342 helix: 1.62 (0.15), residues: 1090 sheet: None (None), residues: 0 loop : -2.17 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 208 HIS 0.001 0.001 HIS T 136 PHE 0.028 0.001 PHE J 62 TYR 0.015 0.002 TYR T 277 ARG 0.007 0.000 ARG T 96 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 876) hydrogen bonds : angle 3.86950 ( 2604) SS BOND : bond 0.01654 ( 1) SS BOND : angle 2.35565 ( 2) covalent geometry : bond 0.00336 (10164) covalent geometry : angle 0.52876 (13833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ILE cc_start: 0.9172 (tp) cc_final: 0.8849 (tp) REVERT: I 2 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8374 (mm-30) REVERT: I 5 ASN cc_start: 0.8753 (p0) cc_final: 0.8501 (p0) REVERT: I 38 ASN cc_start: 0.9036 (t0) cc_final: 0.8703 (t0) REVERT: I 40 GLU cc_start: 0.9000 (tp30) cc_final: 0.8596 (tp30) REVERT: I 48 TYR cc_start: 0.9312 (m-80) cc_final: 0.9103 (m-80) REVERT: J 4 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8692 (mp) REVERT: J 18 ILE cc_start: 0.9018 (mt) cc_final: 0.8803 (mp) REVERT: J 38 ASN cc_start: 0.9207 (t0) cc_final: 0.8981 (t0) REVERT: J 48 TYR cc_start: 0.9107 (m-80) cc_final: 0.8880 (m-80) REVERT: K 1 MET cc_start: 0.7057 (mpt) cc_final: 0.6150 (mpt) REVERT: K 41 ILE cc_start: 0.9540 (tp) cc_final: 0.9280 (tp) REVERT: K 43 ASN cc_start: 0.9178 (p0) cc_final: 0.8908 (p0) REVERT: L 1 MET cc_start: 0.8293 (mtp) cc_final: 0.7792 (mtm) REVERT: M 57 GLU cc_start: 0.8756 (tp30) cc_final: 0.8529 (tp30) REVERT: Q 1 MET cc_start: 0.7645 (tpt) cc_final: 0.6941 (tpt) REVERT: Q 37 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8018 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9092 (t0) cc_final: 0.8464 (t0) REVERT: Z 23 PHE cc_start: 0.7490 (m-80) cc_final: 0.7206 (m-80) REVERT: Z 78 ARG cc_start: 0.4599 (tmt170) cc_final: 0.4339 (tmt170) REVERT: Z 239 GLU cc_start: 0.9217 (tp30) cc_final: 0.8490 (tp30) REVERT: Z 242 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8666 (mttm) REVERT: Y 31 ARG cc_start: 0.9109 (tpp-160) cc_final: 0.8687 (tpp80) REVERT: Y 56 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6444 (mm-30) REVERT: T 59 ASP cc_start: 0.5237 (OUTLIER) cc_final: 0.4625 (m-30) REVERT: T 136 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.5549 (m170) REVERT: T 191 LEU cc_start: 0.7288 (mm) cc_final: 0.5769 (pt) REVERT: T 254 ILE cc_start: 0.8953 (mm) cc_final: 0.8483 (tt) REVERT: T 264 MET cc_start: 0.5420 (tpp) cc_final: 0.5067 (tpp) REVERT: T 272 LEU cc_start: 0.7466 (tp) cc_final: 0.6986 (tt) REVERT: T 291 PHE cc_start: 0.9258 (t80) cc_final: 0.8927 (t80) outliers start: 44 outliers final: 23 residues processed: 328 average time/residue: 0.2112 time to fit residues: 97.7483 Evaluate side-chains 313 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 56.2801 > 50: distance: 35 - 122: 28.536 distance: 38 - 119: 19.976 distance: 62 - 75: 19.826 distance: 66 - 70: 25.656 distance: 67 - 80: 25.715 distance: 70 - 71: 25.345 distance: 71 - 72: 17.626 distance: 71 - 74: 7.890 distance: 72 - 73: 5.898 distance: 72 - 75: 23.430 distance: 75 - 76: 15.565 distance: 76 - 77: 18.458 distance: 76 - 79: 23.608 distance: 77 - 78: 8.129 distance: 77 - 80: 4.747 distance: 80 - 81: 35.017 distance: 81 - 82: 17.987 distance: 81 - 84: 19.992 distance: 82 - 83: 3.680 distance: 82 - 89: 23.537 distance: 84 - 85: 18.710 distance: 85 - 86: 15.473 distance: 86 - 87: 10.198 distance: 86 - 88: 27.738 distance: 89 - 90: 22.953 distance: 90 - 91: 21.879 distance: 91 - 92: 25.516 distance: 91 - 93: 8.773 distance: 93 - 94: 16.254 distance: 94 - 95: 22.962 distance: 94 - 97: 31.125 distance: 95 - 96: 5.090 distance: 95 - 102: 11.245 distance: 97 - 98: 13.716 distance: 98 - 99: 26.288 distance: 99 - 100: 25.628 distance: 100 - 101: 29.152 distance: 102 - 103: 12.724 distance: 103 - 104: 18.055 distance: 103 - 106: 32.198 distance: 104 - 105: 18.559 distance: 104 - 111: 24.621 distance: 106 - 107: 18.901 distance: 107 - 108: 21.226 distance: 108 - 109: 16.238 distance: 109 - 110: 40.974 distance: 111 - 112: 16.802 distance: 112 - 113: 6.334 distance: 112 - 115: 8.135 distance: 113 - 114: 15.787 distance: 113 - 119: 3.646 distance: 115 - 116: 4.569 distance: 116 - 117: 23.288 distance: 116 - 118: 11.897 distance: 119 - 120: 17.539 distance: 120 - 121: 22.053 distance: 120 - 123: 15.579 distance: 121 - 122: 4.758 distance: 121 - 126: 8.711 distance: 123 - 124: 25.744 distance: 123 - 125: 6.030 distance: 126 - 127: 14.584 distance: 126 - 132: 10.566 distance: 127 - 128: 34.617 distance: 127 - 130: 11.877 distance: 128 - 129: 13.232 distance: 128 - 133: 8.034 distance: 130 - 131: 24.759 distance: 131 - 132: 10.712 distance: 133 - 134: 14.770 distance: 134 - 135: 10.246 distance: 134 - 137: 21.526 distance: 135 - 136: 20.620 distance: 135 - 141: 9.280 distance: 137 - 138: 12.737 distance: 138 - 139: 4.121 distance: 138 - 140: 19.248