Starting phenix.real_space_refine on Thu Mar 13 03:15:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2k_38015/03_2025/8x2k_38015_neut.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.086 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 56 5.16 5 C 5440 2.51 5 N 1472 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8570 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1896 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1795 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'LEU%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1803 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {'5YM': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 5.46, per 1000 atoms: 0.64 Number of scatterers: 8570 At special positions: 0 Unit cell: (88.4, 122.4, 124.95, 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 56 16.00 O 1602 8.00 N 1472 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 17 sheets defined 36.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 43 through 68 removed outlier: 3.614A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 102 Processing helix chain 'A' and resid 105 through 140 removed outlier: 3.620A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.278A pdb=" N TYR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.989A pdb=" N GLY A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 230 removed outlier: 3.973A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.510A pdb=" N ALA A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.239A pdb=" N THR A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.934A pdb=" N THR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'B' and resid 13 through 38 removed outlier: 3.998A pdb=" N ALA B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 264 through 278 removed outlier: 4.388A pdb=" N GLU B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.005A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.536A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.931A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 removed outlier: 3.560A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 383 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.581A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.554A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 47 removed outlier: 5.887A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.520A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.578A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.649A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 180 " --> pdb=" O CYS C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 191 through 192 removed outlier: 4.007A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.485A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.513A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 284 through 286 removed outlier: 6.442A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.948A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.948A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.424A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.573A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1128 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: 2.43 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1392 1.30 - 1.43: 2297 1.43 - 1.56: 4964 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8734 Sorted by residual: bond pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.17e-02 7.31e+03 3.23e+01 bond pdb=" C18 5YM A 401 " pdb=" N20 5YM A 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C TYR A 135 " pdb=" O TYR A 135 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.29e-02 6.01e+03 2.49e+01 bond pdb=" C ILE A 208 " pdb=" O ILE A 208 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.13e-02 7.83e+03 1.97e+01 bond pdb=" C PHE A 263 " pdb=" O PHE A 263 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.15e-02 7.56e+03 1.59e+01 ... (remaining 8729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11636 2.39 - 4.77: 169 4.77 - 7.16: 24 7.16 - 9.55: 9 9.55 - 11.93: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 111.81 100.78 11.03 8.60e-01 1.35e+00 1.64e+02 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 114.04 103.06 10.98 1.24e+00 6.50e-01 7.84e+01 angle pdb=" N PRO A 189 " pdb=" CA PRO A 189 " pdb=" CB PRO A 189 " ideal model delta sigma weight residual 103.25 95.34 7.91 1.05e+00 9.07e-01 5.68e+01 angle pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.93e+01 angle pdb=" N ALA A 129 " pdb=" CA ALA A 129 " pdb=" C ALA A 129 " ideal model delta sigma weight residual 113.12 104.57 8.55 1.25e+00 6.40e-01 4.68e+01 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 5065 33.81 - 67.62: 112 67.62 - 101.43: 10 101.43 - 135.24: 0 135.24 - 169.05: 1 Dihedral angle restraints: 5188 sinusoidal: 1981 harmonic: 3207 Sorted by residual: dihedral pdb=" C TYR A 135 " pdb=" N TYR A 135 " pdb=" CA TYR A 135 " pdb=" CB TYR A 135 " ideal model delta harmonic sigma weight residual -122.60 -109.21 -13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N20 5YM A 401 " pdb=" C21 5YM A 401 " pdb=" C22 5YM A 401 " pdb=" O23 5YM A 401 " ideal model delta sinusoidal sigma weight residual -61.92 107.13 -169.05 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CA ALA A 129 " pdb=" CB ALA A 129 " ideal model delta harmonic sigma weight residual 122.90 111.87 11.03 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1246 0.083 - 0.165: 100 0.165 - 0.247: 13 0.247 - 0.330: 3 0.330 - 0.412: 1 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CB VAL A 205 " pdb=" CA VAL A 205 " pdb=" CG1 VAL A 205 " pdb=" CG2 VAL A 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ALA A 129 " pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CB ALA A 129 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1360 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 200 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE A 200 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE A 200 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 162 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C GLY A 162 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 162 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 163 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 113 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C VAL A 113 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL A 113 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 114 " -0.017 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 49 2.51 - 3.11: 6305 3.11 - 3.70: 12259 3.70 - 4.30: 18165 4.30 - 4.90: 31440 Nonbonded interactions: 68218 Sorted by model distance: nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP B 343 " model vdw 1.909 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 1.957 3.040 nonbonded pdb=" O ASP C 228 " pdb=" OG SER C 245 " model vdw 1.979 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.009 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.064 3.040 ... (remaining 68213 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.106 8734 Z= 0.310 Angle : 0.734 11.933 11842 Z= 0.476 Chirality : 0.049 0.412 1363 Planarity : 0.004 0.056 1503 Dihedral : 14.074 169.051 3113 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 0.77 % Allowed : 1.09 % Favored : 98.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.94 % 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: -0.74 (0.25), residues: 1089 helix: 0.30 (0.27), residues: 395 sheet: -0.78 (0.30), residues: 278 loop : -0.88 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 339 HIS 0.003 0.001 HIS B 357 PHE 0.029 0.002 PHE A 202 TYR 0.010 0.001 TYR C 105 ARG 0.012 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.913 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 238 PHE cc_start: 0.7600 (m-10) cc_final: 0.7388 (m-10) REVERT: C 197 ARG cc_start: 0.6720 (mmt90) cc_final: 0.6392 (mmp80) REVERT: E 180 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7167 (mtt180) outliers start: 7 outliers final: 3 residues processed: 139 average time/residue: 0.2693 time to fit residues: 48.3148 Evaluate side-chains 115 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN C 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110365 restraints weight = 10188.488| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.33 r_work: 0.3147 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8734 Z= 0.358 Angle : 0.636 8.231 11842 Z= 0.337 Chirality : 0.046 0.196 1363 Planarity : 0.005 0.056 1503 Dihedral : 7.501 176.914 1227 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.09 % Allowed : 7.99 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1089 helix: 0.54 (0.26), residues: 396 sheet: -0.63 (0.31), residues: 283 loop : -0.90 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 339 HIS 0.005 0.001 HIS B 357 PHE 0.019 0.002 PHE B 222 TYR 0.013 0.002 TYR E 190 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.907 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 378 ASP cc_start: 0.7977 (m-30) cc_final: 0.7765 (m-30) REVERT: C 197 ARG cc_start: 0.7258 (mmt90) cc_final: 0.6510 (mmp80) REVERT: E 180 ARG cc_start: 0.7822 (mtm110) cc_final: 0.6971 (mtt180) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.2619 time to fit residues: 42.4549 Evaluate side-chains 110 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 56.3964 > 50: distance: 64 - 69: 31.306 distance: 69 - 70: 31.292 distance: 70 - 71: 20.263 distance: 70 - 73: 27.723 distance: 71 - 72: 27.783 distance: 71 - 80: 33.277 distance: 73 - 74: 27.330 distance: 74 - 75: 43.529 distance: 75 - 76: 9.393 distance: 76 - 77: 7.142 distance: 77 - 78: 20.886 distance: 77 - 79: 17.782 distance: 81 - 82: 7.342 distance: 81 - 84: 26.813 distance: 82 - 83: 19.580 distance: 82 - 91: 30.126 distance: 84 - 85: 21.164 distance: 85 - 86: 23.896 distance: 85 - 87: 19.775 distance: 86 - 88: 12.834 distance: 87 - 89: 23.577 distance: 88 - 90: 29.323 distance: 89 - 90: 16.478 distance: 91 - 92: 31.144 distance: 91 - 162: 17.878 distance: 92 - 93: 5.978 distance: 92 - 95: 13.223 distance: 93 - 94: 19.753 distance: 93 - 97: 24.482 distance: 94 - 159: 20.519 distance: 95 - 96: 14.045 distance: 97 - 98: 8.395 distance: 98 - 99: 17.384 distance: 99 - 100: 4.359 distance: 99 - 101: 20.821 distance: 101 - 102: 15.312 distance: 102 - 103: 13.954 distance: 102 - 105: 22.227 distance: 103 - 104: 28.948 distance: 103 - 107: 30.456 distance: 105 - 106: 15.293 distance: 107 - 108: 28.579 distance: 108 - 109: 19.957 distance: 109 - 110: 10.360 distance: 109 - 111: 24.021 distance: 111 - 112: 19.198 distance: 112 - 113: 15.806 distance: 112 - 115: 14.624 distance: 113 - 114: 14.211 distance: 113 - 117: 22.760 distance: 115 - 116: 22.361 distance: 117 - 118: 21.533 distance: 118 - 119: 19.227 distance: 119 - 120: 17.322 distance: 119 - 121: 14.286 distance: 121 - 122: 24.917 distance: 122 - 123: 13.358 distance: 122 - 125: 4.829 distance: 123 - 124: 12.103 distance: 123 - 128: 21.710 distance: 125 - 126: 8.062 distance: 125 - 127: 7.555 distance: 128 - 129: 10.196 distance: 129 - 130: 17.856 distance: 129 - 132: 38.044 distance: 130 - 131: 3.833 distance: 130 - 133: 19.534