Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:22:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4d_21040/12_2022/6v4d_21040.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3095 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 2.29, per 1000 atoms: 0.74 Number of scatterers: 3095 At special positions: 0 Unit cell: (67.26, 62.7, 77.52, 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 19 16.00 O 527 8.00 N 509 7.00 C 2040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 880.8 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.617A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.891A pdb=" N ALA A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 149 removed outlier: 4.203A pdb=" N MET A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 137 " --> pdb=" O TRP A 133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.516A pdb=" N TYR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.694A pdb=" N VAL A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.501A pdb=" N ARG A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.603A pdb=" N ILE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.956A pdb=" N CYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 233 removed outlier: 3.612A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.682A pdb=" N GLN A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.873A pdb=" N TYR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.663A pdb=" N THR A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 337 removed outlier: 4.046A pdb=" N TYR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.932A pdb=" N PHE A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Proline residue: A 364 - end of helix removed outlier: 3.736A pdb=" N ARG A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.715A pdb=" N MET A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.665A pdb=" N ALA A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.021A pdb=" N ASP A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 468 removed outlier: 3.756A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Proline residue: A 461 - end of helix removed outlier: 3.913A pdb=" N THR A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 497 removed outlier: 3.868A pdb=" N TRP A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 497 " --> pdb=" O PHE A 493 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 525 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: 0.76 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 714 1.33 - 1.45: 728 1.45 - 1.57: 1710 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3182 Sorted by residual: bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.19e+01 bond pdb=" N VAL A 96 " pdb=" CA VAL A 96 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.83e+00 bond pdb=" N ILE A 87 " pdb=" CA ILE A 87 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.53e+00 bond pdb=" N VAL A 124 " pdb=" CA VAL A 124 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.32e+00 bond pdb=" N ILE A 140 " pdb=" CA ILE A 140 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.23e-02 6.61e+03 6.43e+00 ... (remaining 3177 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.89: 103 106.89 - 113.71: 1777 113.71 - 120.52: 1358 120.52 - 127.33: 1068 127.33 - 134.15: 43 Bond angle restraints: 4349 Sorted by residual: angle pdb=" C GLN A 139 " pdb=" CA GLN A 139 " pdb=" CB GLN A 139 " ideal model delta sigma weight residual 110.88 104.09 6.79 1.57e+00 4.06e-01 1.87e+01 angle pdb=" C PRO A 141 " pdb=" CA PRO A 141 " pdb=" CB PRO A 141 " ideal model delta sigma weight residual 113.06 106.54 6.52 1.59e+00 3.96e-01 1.68e+01 angle pdb=" CA ILE A 127 " pdb=" C ILE A 127 " pdb=" O ILE A 127 " ideal model delta sigma weight residual 120.95 116.93 4.02 1.04e+00 9.25e-01 1.50e+01 angle pdb=" N GLN A 139 " pdb=" CA GLN A 139 " pdb=" C GLN A 139 " ideal model delta sigma weight residual 111.07 115.12 -4.05 1.07e+00 8.73e-01 1.44e+01 angle pdb=" O ASN A 433 " pdb=" C ASN A 433 " pdb=" N HIS A 434 " ideal model delta sigma weight residual 122.12 126.04 -3.92 1.06e+00 8.90e-01 1.37e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1597 16.04 - 32.08: 149 32.08 - 48.11: 40 48.11 - 64.15: 3 64.15 - 80.19: 2 Dihedral angle restraints: 1791 sinusoidal: 594 harmonic: 1197 Sorted by residual: dihedral pdb=" CD ARG A 88 " pdb=" NE ARG A 88 " pdb=" CZ ARG A 88 " pdb=" NH1 ARG A 88 " ideal model delta sinusoidal sigma weight residual 0.00 36.82 -36.82 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CA PHE A 65 " pdb=" C PHE A 65 " pdb=" N GLY A 66 " pdb=" CA GLY A 66 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C ILE A 127 " pdb=" N ILE A 127 " pdb=" CA ILE A 127 " pdb=" CB ILE A 127 " ideal model delta harmonic sigma weight residual -122.00 -130.15 8.15 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 1788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 352 0.052 - 0.104: 119 0.104 - 0.156: 20 0.156 - 0.208: 8 0.208 - 0.260: 3 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA VAL A 432 " pdb=" N VAL A 432 " pdb=" C VAL A 432 " pdb=" CB VAL A 432 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 127 " pdb=" CA ILE A 127 " pdb=" CG1 ILE A 127 " pdb=" CG2 ILE A 127 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 499 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 88 " -0.650 9.50e-02 1.11e+02 2.91e-01 5.17e+01 pdb=" NE ARG A 88 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 88 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 88 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 88 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 430 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C PHE A 430 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 430 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 431 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 503 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 504 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " -0.031 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 13 2.38 - 3.01: 2195 3.01 - 3.64: 4698 3.64 - 4.27: 6454 4.27 - 4.90: 10260 Nonbonded interactions: 23620 Sorted by model distance: nonbonded pdb=" O ILE A 127 " pdb=" OG SER A 130 " model vdw 1.752 2.440 nonbonded pdb=" O PHE A 85 " pdb=" CD1 PHE A 85 " model vdw 2.034 3.340 nonbonded pdb=" O GLU A 191 " pdb=" OG1 THR A 194 " model vdw 2.098 2.440 nonbonded pdb=" O LEU A 168 " pdb=" OG SER A 171 " model vdw 2.158 2.440 nonbonded pdb=" OG SER A 332 " pdb=" OE1 GLN A 333 " model vdw 2.159 2.440 ... (remaining 23615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2040 2.51 5 N 509 2.21 5 O 527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.000 Extract box with map and model: 3.770 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.007 0.039 3182 Z= 0.476 Angle : 0.901 7.256 4349 Z= 0.582 Chirality : 0.057 0.260 502 Planarity : 0.014 0.291 540 Dihedral : 13.633 80.188 1031 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 1.35 % 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: -3.84 (0.36), residues: 416 helix: -1.95 (0.26), residues: 268 sheet: None (None), residues: 0 loop : -3.53 (0.49), residues: 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 172 average time/residue: 0.1149 time to fit residues: 24.5959 Evaluate side-chains 137 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0323 time to fit residues: 0.6215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 187 GLN A 199 HIS A 238 GLN A 356 HIS A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3182 Z= 0.205 Angle : 0.702 6.938 4349 Z= 0.356 Chirality : 0.044 0.144 502 Planarity : 0.005 0.051 540 Dihedral : 4.752 17.209 451 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 5.41 % 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: -1.78 (0.40), residues: 416 helix: -0.22 (0.30), residues: 269 sheet: None (None), residues: 0 loop : -3.01 (0.50), residues: 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 169 average time/residue: 0.1037 time to fit residues: 22.2830 Evaluate side-chains 150 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0325 time to fit residues: 0.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 187 GLN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3182 Z= 0.213 Angle : 0.712 13.822 4349 Z= 0.356 Chirality : 0.045 0.175 502 Planarity : 0.005 0.054 540 Dihedral : 4.718 16.711 451 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 3.72 % 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: -1.11 (0.42), residues: 416 helix: 0.32 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -2.72 (0.52), residues: 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 170 average time/residue: 0.1075 time to fit residues: 22.9849 Evaluate side-chains 153 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0321 time to fit residues: 0.5302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 3182 Z= 0.202 Angle : 0.719 12.543 4349 Z= 0.356 Chirality : 0.045 0.167 502 Planarity : 0.005 0.037 540 Dihedral : 4.597 16.186 451 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 4.39 % 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: -0.93 (0.42), residues: 416 helix: 0.45 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -2.64 (0.53), residues: 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.334 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 172 average time/residue: 0.1122 time to fit residues: 24.2412 Evaluate side-chains 165 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0349 time to fit residues: 0.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 3182 Z= 0.197 Angle : 0.723 12.453 4349 Z= 0.357 Chirality : 0.045 0.209 502 Planarity : 0.005 0.042 540 Dihedral : 4.489 16.099 451 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 2.36 % 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: -0.72 (0.43), residues: 416 helix: 0.61 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -2.41 (0.53), residues: 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 172 average time/residue: 0.1204 time to fit residues: 25.5807 Evaluate side-chains 156 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0322 time to fit residues: 0.5712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0370 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3182 Z= 0.204 Angle : 0.751 12.866 4349 Z= 0.368 Chirality : 0.046 0.209 502 Planarity : 0.005 0.042 540 Dihedral : 4.475 16.706 451 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 3.04 % 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: -0.71 (0.42), residues: 416 helix: 0.61 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -2.41 (0.52), residues: 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 0.351 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.1089 time to fit residues: 23.0011 Evaluate side-chains 157 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0299 time to fit residues: 0.5789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7774 > 50: distance: 37 - 65: 4.978 distance: 43 - 49: 7.899 distance: 49 - 50: 13.781 distance: 50 - 51: 16.933 distance: 50 - 53: 9.171 distance: 51 - 52: 10.747 distance: 51 - 56: 17.444 distance: 53 - 54: 31.747 distance: 53 - 55: 9.512 distance: 56 - 57: 8.581 distance: 57 - 58: 10.142 distance: 57 - 60: 16.050 distance: 58 - 59: 7.179 distance: 58 - 65: 11.431 distance: 60 - 61: 11.375 distance: 61 - 62: 13.954 distance: 62 - 63: 4.387 distance: 62 - 64: 5.533 distance: 65 - 66: 11.769 distance: 66 - 67: 5.213 distance: 66 - 69: 6.514 distance: 67 - 68: 24.642 distance: 67 - 70: 19.128 distance: 70 - 71: 9.478 distance: 71 - 72: 26.368 distance: 71 - 74: 24.727 distance: 72 - 73: 37.865 distance: 72 - 75: 25.674 distance: 75 - 76: 33.219 distance: 76 - 77: 52.516 distance: 77 - 78: 41.407 distance: 77 - 79: 22.843 distance: 79 - 80: 16.682 distance: 80 - 81: 8.352 distance: 80 - 83: 10.027 distance: 81 - 82: 6.669 distance: 81 - 93: 6.998 distance: 83 - 84: 15.906 distance: 84 - 85: 9.645 distance: 84 - 86: 12.901 distance: 86 - 88: 6.164 distance: 86 - 89: 9.530 distance: 87 - 88: 5.045 distance: 88 - 90: 8.099 distance: 89 - 91: 12.299 distance: 90 - 92: 5.555 distance: 93 - 94: 10.391 distance: 94 - 95: 13.294 distance: 94 - 97: 19.883 distance: 95 - 96: 17.112 distance: 95 - 99: 12.389 distance: 96 - 123: 9.760 distance: 97 - 98: 14.915 distance: 99 - 100: 11.014 distance: 100 - 101: 8.769 distance: 100 - 103: 12.863 distance: 101 - 102: 12.761 distance: 101 - 105: 13.768 distance: 102 - 135: 8.272 distance: 103 - 104: 15.846 distance: 105 - 106: 7.539 distance: 106 - 107: 9.169 distance: 106 - 109: 16.460 distance: 107 - 108: 10.090 distance: 107 - 112: 10.010 distance: 109 - 110: 10.341 distance: 109 - 111: 23.397 distance: 112 - 113: 13.388 distance: 113 - 114: 10.633 distance: 113 - 116: 16.807 distance: 114 - 115: 12.788 distance: 115 - 149: 15.585 distance: 116 - 117: 9.815 distance: 117 - 118: 12.513 distance: 117 - 119: 11.429 distance: 118 - 120: 7.935 distance: 119 - 121: 7.676 distance: 120 - 122: 13.737 distance: 121 - 122: 11.602