Starting phenix.real_space_refine on Thu Jan 16 01:36:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fee_50339/01_2025/9fee_50339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fee_50339/01_2025/9fee_50339.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/9fee_50339/01_2025/9fee_50339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fee_50339/01_2025/9fee_50339.map" model { file = "/net/cci-nas-00/data/ceres_data/9fee_50339/01_2025/9fee_50339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fee_50339/01_2025/9fee_50339.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= 0.002 sd= 0.033 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 48 5.16 5 C 5818 2.51 5 N 1568 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2291 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2267 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2262 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2292 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 310, 2286 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 310, 2286 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 bond proxies already assigned to first conformer: 2318 Time building chain proxies: 6.66, per 1000 atoms: 0.73 Number of scatterers: 9112 At special positions: 0 Unit cell: (91.16, 103.2, 103.2, 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 48 16.00 O 1678 8.00 N 1568 7.00 C 5818 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 - 3.00 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 48.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.607A pdb=" N GLN A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.077A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.283A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.508A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.521A pdb=" N GLU A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.578A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.806A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.830A pdb=" N ASP B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.759A pdb=" N THR B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.676A pdb=" N GLY B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix removed outlier: 3.505A pdb=" N ALA B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 169 removed outlier: 4.402A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.640A pdb=" N GLN B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.949A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.684A pdb=" N MET B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 319 removed outlier: 3.800A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 4.163A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.715A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.596A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.573A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 3.560A pdb=" N LYS C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 4.347A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.856A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.503A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.698A pdb=" N HIS C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 318 removed outlier: 3.599A pdb=" N GLY C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 4.013A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.850A pdb=" N ASP D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.857A pdb=" N GLU D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 76' Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.614A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix removed outlier: 3.692A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 206 through 225 removed outlier: 3.802A pdb=" N GLN D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 3.533A pdb=" N MET D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 317 removed outlier: 3.811A pdb=" N MET D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.292A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 123 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.878A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.690A pdb=" N LEU B 33 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B 82 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 261 removed outlier: 3.778A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.325A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 261 removed outlier: 3.557A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 59 removed outlier: 3.964A pdb=" N LEU D 33 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 261 removed outlier: 3.577A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1236 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: 2.50 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3006 1.34 - 1.46: 1397 1.46 - 1.58: 4786 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 9269 Sorted by residual: bond pdb=" C HIS A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.20e-03 1.49e+04 6.89e+00 bond pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta sigma weight residual 1.465 1.490 -0.025 2.03e-02 2.43e+03 1.53e+00 bond pdb=" C LEU B 63 " pdb=" N PRO B 64 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.18e-02 7.18e+03 1.44e+00 bond pdb=" C ARG C 68 " pdb=" N ASP C 69 " ideal model delta sigma weight residual 1.333 1.363 -0.031 2.74e-02 1.33e+03 1.26e+00 bond pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.17e-01 ... (remaining 9264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12293 1.50 - 3.01: 274 3.01 - 4.51: 41 4.51 - 6.01: 16 6.01 - 7.52: 6 Bond angle restraints: 12630 Sorted by residual: angle pdb=" C GLU B 267 " pdb=" CA GLU B 267 " pdb=" CB GLU B 267 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" CA GLU B 267 " pdb=" C GLU B 267 " pdb=" N HIS B 268 " ideal model delta sigma weight residual 119.52 116.27 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N VAL C 126 " pdb=" CA VAL C 126 " pdb=" C VAL C 126 " ideal model delta sigma weight residual 113.47 109.49 3.98 1.01e+00 9.80e-01 1.55e+01 angle pdb=" C VAL B 191 " pdb=" CA VAL B 191 " pdb=" CB VAL B 191 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.01e+00 9.80e-01 1.01e+01 angle pdb=" C HIS D 185 " pdb=" N BSER D 186 " pdb=" CA BSER D 186 " ideal model delta sigma weight residual 121.54 115.61 5.93 1.91e+00 2.74e-01 9.65e+00 ... (remaining 12625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4900 17.85 - 35.69: 579 35.69 - 53.54: 136 53.54 - 71.39: 18 71.39 - 89.23: 5 Dihedral angle restraints: 5638 sinusoidal: 2142 harmonic: 3496 Sorted by residual: dihedral pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" N PRO B 65 " pdb=" CA PRO B 65 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PRO A 64 " pdb=" C PRO A 64 " pdb=" N PRO A 65 " pdb=" CA PRO A 65 " ideal model delta harmonic sigma weight residual 180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 764 0.027 - 0.054: 471 0.054 - 0.081: 159 0.081 - 0.108: 121 0.108 - 0.135: 44 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA VAL C 66 " pdb=" N VAL C 66 " pdb=" C VAL C 66 " pdb=" CB VAL C 66 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1556 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 66 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO C 67 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 191 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 192 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 66 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 67 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.022 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1490 2.76 - 3.29: 8341 3.29 - 3.83: 13738 3.83 - 4.36: 16069 4.36 - 4.90: 29062 Nonbonded interactions: 68700 Sorted by model distance: nonbonded pdb=" OD1 ASN B 131 " pdb=" OG SER B 186 " model vdw 2.225 3.040 nonbonded pdb=" O LEU B 112 " pdb=" OG SER B 116 " model vdw 2.242 3.040 nonbonded pdb=" O SER A 156 " pdb=" OG SER A 156 " model vdw 2.248 3.040 nonbonded pdb=" O ALA D 76 " pdb=" OG SER D 118 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 313 " pdb=" OG1 THR A 317 " model vdw 2.266 3.040 ... (remaining 68695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 88 or resid 100 through 185 or resid 187 through \ 318)) selection = (chain 'B' and (resid 1 through 185 or resid 187 through 318)) selection = (chain 'C' and (resid 1 through 185 or resid 187 through 318)) selection = (chain 'D' and (resid 1 through 88 or resid 100 through 185 or resid 187 through \ 318)) } 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=0.00 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: 1.140 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.990 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.004 0.045 9269 Z= 0.242 Angle : 0.582 7.517 12630 Z= 0.311 Chirality : 0.046 0.135 1559 Planarity : 0.005 0.043 1621 Dihedral : 15.800 89.231 3396 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.20 % Allowed : 25.55 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.40 (0.23), residues: 1223 helix: 0.10 (0.22), residues: 534 sheet: -1.24 (0.42), residues: 151 loop : -1.88 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 58 PHE 0.012 0.001 PHE D 27 TYR 0.010 0.001 TYR D 261 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.020 Fit side-chains REVERT: B 263 ASP cc_start: 0.7936 (t70) cc_final: 0.7667 (t70) outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.2236 time to fit residues: 25.8582 Evaluate side-chains 74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN C 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097323 restraints weight = 18365.410| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.74 r_work: 0.3055 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9269 Z= 0.290 Angle : 0.633 6.042 12630 Z= 0.336 Chirality : 0.048 0.146 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.736 28.261 1308 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.32 % Allowed : 23.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.60 (0.24), residues: 1223 helix: 1.13 (0.23), residues: 542 sheet: -0.77 (0.40), residues: 171 loop : -2.00 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 245 PHE 0.013 0.002 PHE D 27 TYR 0.008 0.001 TYR D 261 ARG 0.004 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.030 Fit side-chains REVERT: B 7 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8008 (mm) REVERT: C 303 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: D 51 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7644 (tpt-90) outliers start: 33 outliers final: 20 residues processed: 100 average time/residue: 0.1916 time to fit residues: 27.8107 Evaluate side-chains 90 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 70.3341 > 50: distance: 97 - 141: 35.307 distance: 108 - 132: 31.193 distance: 110 - 112: 34.094 distance: 111 - 129: 37.312 distance: 112 - 113: 39.862 distance: 113 - 114: 44.648 distance: 114 - 115: 44.989 distance: 114 - 121: 19.857 distance: 116 - 117: 68.990 distance: 117 - 118: 57.887 distance: 118 - 119: 40.981 distance: 119 - 120: 68.976 distance: 122 - 123: 39.081 distance: 122 - 125: 3.970 distance: 123 - 124: 41.135 distance: 125 - 126: 27.466 distance: 126 - 127: 49.831 distance: 126 - 128: 48.437 distance: 129 - 130: 39.931 distance: 130 - 131: 31.592 distance: 131 - 132: 32.548 distance: 131 - 133: 9.175 distance: 133 - 134: 38.746 distance: 134 - 135: 40.579 distance: 134 - 137: 39.279 distance: 137 - 138: 56.779 distance: 137 - 139: 41.216 distance: 138 - 140: 11.401 distance: 143 - 144: 39.154 distance: 143 - 150: 39.972 distance: 145 - 146: 57.301 distance: 150 - 151: 40.365 distance: 151 - 152: 56.456 distance: 151 - 154: 39.838 distance: 152 - 153: 39.633 distance: 152 - 161: 40.539 distance: 154 - 155: 41.258 distance: 157 - 158: 39.308 distance: 158 - 160: 40.544 distance: 162 - 163: 70.063 distance: 162 - 165: 39.676 distance: 163 - 164: 39.733 distance: 163 - 172: 56.565 distance: 165 - 166: 38.895 distance: 166 - 167: 33.180 distance: 167 - 168: 33.526 distance: 168 - 169: 16.755 distance: 169 - 170: 12.896 distance: 169 - 171: 23.958 distance: 173 - 174: 55.091 distance: 173 - 176: 37.961 distance: 174 - 175: 40.046 distance: 174 - 180: 40.019 distance: 177 - 179: 64.740 distance: 181 - 182: 38.645 distance: 181 - 184: 41.512 distance: 182 - 183: 40.394 distance: 184 - 185: 12.533 distance: 185 - 186: 39.018 distance: 188 - 189: 44.813 distance: 188 - 191: 21.057 distance: 189 - 190: 28.907 distance: 189 - 195: 22.353 distance: 191 - 193: 43.311 distance: 192 - 194: 14.741