Starting phenix.real_space_refine on Thu Oct 10 04:58:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/10_2024/9bkj_44642.cif" } resolution = 2.59 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= 0.005 sd= 0.103 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 57 5.16 5 C 4357 2.51 5 N 1150 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 6795 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2483 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 3, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 396 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1604 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 63 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.25, per 1000 atoms: 0.63 Number of scatterers: 6795 At special positions: 0 Unit cell: (88.4, 88.4, 127.5, 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 57 16.00 O 1231 8.00 N 1150 7.00 C 4357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.07 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 47.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 74 through 104 removed outlier: 3.528A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Proline residue: R 96 - end of helix removed outlier: 3.975A pdb=" N ILE R 100 " --> pdb=" O PRO R 96 " (cutoff:3.500A) Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.940A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 238 removed outlier: 3.578A pdb=" N PHE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Proline residue: R 221 - end of helix Processing helix chain 'R' and resid 306 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 339 through 348 Processing helix chain 'R' and resid 349 through 371 removed outlier: 4.214A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.652A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.172A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.540A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.818A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.533A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.406A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.746A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.915A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.720A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.457A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.419A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 181 Processing sheet with id=AA9, first strand: chain 'R' and resid 185 through 186 Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1101 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: 1.98 Time building geometry restraints manager: 2.26 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: 1442 1.33 - 1.45: 1594 1.45 - 1.58: 3809 1.58 - 1.70: 1 1.70 - 1.82: 84 Bond restraints: 6930 Sorted by residual: bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.583 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.56e-02 4.11e+03 1.20e+01 bond pdb=" CA ALA B 56 " pdb=" CB ALA B 56 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.35e-02 5.49e+03 1.10e+01 bond pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.88e+00 bond pdb=" N ASN R 98 " pdb=" CA ASN R 98 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.49e+00 ... (remaining 6925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8961 1.56 - 3.12: 355 3.12 - 4.68: 82 4.68 - 6.24: 16 6.24 - 7.80: 6 Bond angle restraints: 9420 Sorted by residual: angle pdb=" N CYS R 196 " pdb=" CA CYS R 196 " pdb=" C CYS R 196 " ideal model delta sigma weight residual 110.42 103.21 7.21 1.46e+00 4.69e-01 2.44e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.18 107.51 5.67 1.21e+00 6.83e-01 2.20e+01 angle pdb=" C MET P 6 " pdb=" N ASP P 7 " pdb=" CA ASP P 7 " ideal model delta sigma weight residual 120.38 126.24 -5.86 1.37e+00 5.33e-01 1.83e+01 angle pdb=" CA PHE R 185 " pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 121.33 116.84 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" C MET R 173 " pdb=" N THR R 174 " pdb=" CA THR R 174 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.68e+01 ... (remaining 9415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3766 17.92 - 35.84: 281 35.84 - 53.75: 44 53.75 - 71.67: 6 71.67 - 89.59: 2 Dihedral angle restraints: 4099 sinusoidal: 1496 harmonic: 2603 Sorted by residual: dihedral pdb=" CA CYS R 94 " pdb=" C CYS R 94 " pdb=" N MET R 95 " pdb=" CA MET R 95 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE R 218 " pdb=" C PHE R 218 " pdb=" N LEU R 219 " pdb=" CA LEU R 219 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LEU R 215 " pdb=" C LEU R 215 " pdb=" N ILE R 216 " pdb=" CA ILE R 216 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 787 0.042 - 0.084: 225 0.084 - 0.126: 88 0.126 - 0.168: 12 0.168 - 0.210: 2 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA TRP P 5 " pdb=" N TRP P 5 " pdb=" C TRP P 5 " pdb=" CB TRP P 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU R 99 " pdb=" N LEU R 99 " pdb=" C LEU R 99 " pdb=" CB LEU R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET R 72 " pdb=" N MET R 72 " pdb=" C MET R 72 " pdb=" CB MET R 72 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1111 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 329 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C THR B 329 " -0.035 2.00e-02 2.50e+03 pdb=" O THR B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 330 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 184 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PRO R 184 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO R 184 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE R 185 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 196 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C CYS R 196 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS R 196 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG R 197 " 0.011 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1556 2.79 - 3.32: 6533 3.32 - 3.84: 11364 3.84 - 4.37: 13717 4.37 - 4.90: 23585 Nonbonded interactions: 56755 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.260 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 3.040 nonbonded pdb=" NZ LYS B 280 " pdb=" O ASP B 322 " model vdw 2.296 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.343 3.120 ... (remaining 56750 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 ========== 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 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: 0.960 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:15.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 0.096 6930 Z= 0.299 Angle : 0.754 7.797 9420 Z= 0.475 Chirality : 0.046 0.210 1114 Planarity : 0.004 0.032 1178 Dihedral : 12.935 89.589 2398 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.96 % Favored : 97.81 % Rotamer: Outliers : 0.71 % Allowed : 1.13 % Favored : 98.16 % 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: 1.02 (0.29), residues: 869 helix: 2.14 (0.26), residues: 383 sheet: 0.40 (0.39), residues: 171 loop : -1.03 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.020 0.001 PHE R 185 TYR 0.007 0.001 TYR B 289 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.652 Fit side-chains REVERT: B 195 ASP cc_start: 0.6424 (p0) cc_final: 0.6090 (p0) outliers start: 5 outliers final: 1 residues processed: 117 average time/residue: 1.4536 time to fit residues: 177.4616 Evaluate side-chains 98 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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: 63.7397 > 50: distance: 3 - 27: 3.513 distance: 10 - 35: 5.375 distance: 17 - 39: 7.193 distance: 22 - 27: 3.078 distance: 23 - 47: 20.805 distance: 27 - 28: 4.756 distance: 28 - 29: 6.281 distance: 28 - 31: 10.132 distance: 29 - 30: 10.612 distance: 29 - 35: 7.512 distance: 30 - 54: 28.633 distance: 31 - 32: 14.197 distance: 32 - 33: 21.718 distance: 32 - 34: 24.121 distance: 35 - 36: 6.521 distance: 36 - 37: 12.441 distance: 37 - 38: 13.929 distance: 37 - 39: 4.936 distance: 38 - 62: 15.232 distance: 39 - 40: 9.475 distance: 40 - 41: 11.233 distance: 40 - 43: 11.452 distance: 41 - 42: 14.702 distance: 41 - 47: 9.640 distance: 42 - 69: 63.740 distance: 43 - 44: 13.437 distance: 44 - 45: 5.236 distance: 44 - 46: 13.374 distance: 47 - 48: 12.786 distance: 48 - 49: 18.585 distance: 48 - 51: 10.552 distance: 49 - 50: 18.438 distance: 49 - 54: 11.735 distance: 50 - 77: 37.882 distance: 51 - 52: 22.078 distance: 51 - 53: 3.785 distance: 54 - 55: 5.744 distance: 55 - 56: 6.582 distance: 55 - 58: 10.872 distance: 56 - 57: 7.803 distance: 56 - 62: 4.211 distance: 57 - 84: 21.209 distance: 58 - 59: 24.762 distance: 59 - 60: 14.980 distance: 59 - 61: 6.367 distance: 62 - 63: 16.250 distance: 63 - 64: 29.110 distance: 63 - 66: 13.946 distance: 64 - 65: 22.665 distance: 64 - 69: 34.836 distance: 65 - 91: 27.048 distance: 66 - 67: 27.581 distance: 66 - 68: 27.411 distance: 69 - 70: 31.598 distance: 70 - 71: 14.099 distance: 70 - 73: 16.139 distance: 71 - 72: 4.819 distance: 71 - 77: 8.245 distance: 72 - 99: 28.916 distance: 73 - 74: 15.177 distance: 74 - 76: 8.489 distance: 77 - 78: 14.714 distance: 78 - 79: 10.110 distance: 78 - 81: 10.000 distance: 79 - 80: 6.703 distance: 80 - 106: 10.737 distance: 81 - 82: 9.573 distance: 81 - 83: 32.168 distance: 84 - 85: 3.502 distance: 85 - 86: 3.119 distance: 85 - 88: 5.978 distance: 86 - 87: 4.404 distance: 87 - 114: 4.489 distance: 88 - 89: 15.110 distance: 88 - 90: 8.970 distance: 92 - 93: 8.411 distance: 92 - 95: 8.581 distance: 93 - 94: 13.044 distance: 93 - 99: 9.400 distance: 95 - 96: 18.322 distance: 96 - 97: 23.651 distance: 96 - 98: 21.797 distance: 179 - 188: 3.049