Starting phenix.real_space_refine on Sun May 11 03:58:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.map" model { file = "/net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j13_61066/05_2025/9j13_61066.cif" } resolution = 3.4 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= 0.042 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 4828 2.51 5 N 1192 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7440 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3720 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 487} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: B Time building chain proxies: 5.63, per 1000 atoms: 0.76 Number of scatterers: 7440 At special positions: 0 Unit cell: (111.1, 104.5, 88, 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 1364 8.00 N 1192 7.00 C 4828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=1.73 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=1.73 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 64.0% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 removed outlier: 3.876A pdb=" N LYS A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 12 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.623A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 55 removed outlier: 3.810A pdb=" N GLU A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.024A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 95 through 129 removed outlier: 3.661A pdb=" N VAL A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.998A pdb=" N TYR A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.543A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.590A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 removed outlier: 4.189A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.913A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.659A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.587A pdb=" N VAL A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.754A pdb=" N ALA A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.806A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.571A pdb=" N GLY A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.935A pdb=" N ASN A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 Proline residue: A 440 - end of helix removed outlier: 3.813A pdb=" N VAL A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 461 through 477 removed outlier: 3.633A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.710A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.742A pdb=" N GLY A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.791A pdb=" N TRP B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 12 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.623A pdb=" N ARG B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 55 removed outlier: 3.811A pdb=" N GLU B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.024A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 95 through 129 removed outlier: 3.661A pdb=" N VAL B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.999A pdb=" N TYR B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 178 removed outlier: 3.543A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.590A pdb=" N ARG B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 4.189A pdb=" N ALA B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.913A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.658A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.587A pdb=" N VAL B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.754A pdb=" N ALA B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.807A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 423 removed outlier: 3.571A pdb=" N GLY B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.936A pdb=" N ASN B 432 " --> pdb=" O PRO B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 Proline residue: B 440 - end of helix removed outlier: 3.812A pdb=" N VAL B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.633A pdb=" N ALA B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.711A pdb=" N ILE B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 495 " --> pdb=" O TYR B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 removed outlier: 3.742A pdb=" N GLY B 502 " --> pdb=" O ASP B 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.570A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 7.289A pdb=" N GLU A 234 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.570A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 235 removed outlier: 7.288A pdb=" N GLU B 234 " --> pdb=" O LEU B 243 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1032 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: 1.84 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2300 1.34 - 1.46: 1683 1.46 - 1.58: 3513 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7590 Sorted by residual: bond pdb=" C THR A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.334 1.353 -0.019 1.51e-02 4.39e+03 1.61e+00 bond pdb=" C THR B 427 " pdb=" N PRO B 428 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.46e+00 bond pdb=" N ILE A 57 " pdb=" CA ILE A 57 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" N ILE B 57 " pdb=" CA ILE B 57 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.06e+00 bond pdb=" CA ILE A 57 " pdb=" CB ILE A 57 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.42e-02 4.96e+03 9.41e-01 ... (remaining 7585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 10290 3.90 - 7.80: 24 7.80 - 11.70: 0 11.70 - 15.61: 0 15.61 - 19.51: 4 Bond angle restraints: 10318 Sorted by residual: angle pdb=" C ASP A 365 " pdb=" CA ASP A 365 " pdb=" CB ASP A 365 " ideal model delta sigma weight residual 110.74 130.25 -19.51 1.66e+00 3.63e-01 1.38e+02 angle pdb=" C ASP B 365 " pdb=" CA ASP B 365 " pdb=" CB ASP B 365 " ideal model delta sigma weight residual 110.74 130.22 -19.48 1.66e+00 3.63e-01 1.38e+02 angle pdb=" N GLY B 366 " pdb=" CA GLY B 366 " pdb=" C GLY B 366 " ideal model delta sigma weight residual 110.18 94.13 16.05 1.56e+00 4.11e-01 1.06e+02 angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 110.18 94.13 16.05 1.56e+00 4.11e-01 1.06e+02 angle pdb=" C ILE A 261 " pdb=" CA ILE A 261 " pdb=" CB ILE A 261 " ideal model delta sigma weight residual 112.22 108.43 3.79 1.38e+00 5.25e-01 7.54e+00 ... (remaining 10313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.67: 3891 13.67 - 27.34: 361 27.34 - 41.01: 138 41.01 - 54.68: 26 54.68 - 68.35: 12 Dihedral angle restraints: 4428 sinusoidal: 1590 harmonic: 2838 Sorted by residual: dihedral pdb=" C ASP B 365 " pdb=" N ASP B 365 " pdb=" CA ASP B 365 " pdb=" CB ASP B 365 " ideal model delta harmonic sigma weight residual -122.60 -158.16 35.56 0 2.50e+00 1.60e-01 2.02e+02 dihedral pdb=" C ASP A 365 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " pdb=" CB ASP A 365 " ideal model delta harmonic sigma weight residual -122.60 -158.14 35.54 0 2.50e+00 1.60e-01 2.02e+02 dihedral pdb=" N ASP B 365 " pdb=" C ASP B 365 " pdb=" CA ASP B 365 " pdb=" CB ASP B 365 " ideal model delta harmonic sigma weight residual 122.80 152.92 -30.12 0 2.50e+00 1.60e-01 1.45e+02 ... (remaining 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1250 0.286 - 0.572: 0 0.572 - 0.858: 0 0.858 - 1.144: 0 1.144 - 1.430: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ASP B 365 " pdb=" N ASP B 365 " pdb=" C ASP B 365 " pdb=" CB ASP B 365 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" CA ASP A 365 " pdb=" N ASP A 365 " pdb=" C ASP A 365 " pdb=" CB ASP A 365 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" CB ILE A 57 " pdb=" CA ILE A 57 " pdb=" CG1 ILE A 57 " pdb=" CG2 ILE A 57 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1249 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 427 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO A 428 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 427 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 428 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 439 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 440 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.019 5.00e-02 4.00e+02 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 116 2.69 - 3.24: 7503 3.24 - 3.80: 10799 3.80 - 4.35: 14130 4.35 - 4.90: 23905 Nonbonded interactions: 56453 Sorted by model distance: nonbonded pdb=" O VAL B 281 " pdb=" OG SER B 285 " model vdw 2.139 3.040 nonbonded pdb=" O VAL A 281 " pdb=" OG SER A 285 " model vdw 2.139 3.040 nonbonded pdb=" OG SER B 78 " pdb=" OD1 ASN B 95 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 78 " pdb=" OD1 ASN A 95 " model vdw 2.243 3.040 nonbonded pdb=" O LEU B 473 " pdb=" OG1 THR B 477 " model vdw 2.272 3.040 ... (remaining 56448 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.830 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.840 Find NCS groups from input model: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.006 0.305 7596 Z= 0.283 Angle : 0.867 28.561 10330 Z= 0.503 Chirality : 0.070 1.430 1252 Planarity : 0.004 0.049 1270 Dihedral : 13.296 68.345 2610 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.25 % Allowed : 12.66 % Favored : 87.09 % Cbeta Deviations : 0.22 % 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: -1.46 (0.27), residues: 1004 helix: 0.24 (0.24), residues: 536 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.001 0.000 HIS A 315 PHE 0.013 0.001 PHE B 132 TYR 0.007 0.001 TYR B 305 ARG 0.004 0.000 ARG A 187 Details of bonding type rmsd hydrogen bonds : bond 0.21552 ( 348) hydrogen bonds : angle 6.34106 ( 1032) SS BOND : bond 0.17608 ( 6) SS BOND : angle 12.94016 ( 12) covalent geometry : bond 0.00269 ( 7590) covalent geometry : angle 0.74637 (10318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.8907 (m) cc_final: 0.8631 (m) outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 0.1956 time to fit residues: 27.2641 Evaluate side-chains 92 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108344 restraints weight = 10801.310| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.74 r_work: 0.3142 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7596 Z= 0.195 Angle : 0.607 5.290 10330 Z= 0.320 Chirality : 0.043 0.148 1252 Planarity : 0.004 0.048 1270 Dihedral : 4.639 17.207 1064 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.91 % Allowed : 11.65 % Favored : 85.44 % 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: -1.43 (0.27), residues: 1004 helix: 0.44 (0.24), residues: 550 sheet: -3.17 (0.83), residues: 20 loop : -2.77 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B 315 PHE 0.016 0.002 PHE A 132 TYR 0.012 0.002 TYR B 276 ARG 0.003 0.001 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 348) hydrogen bonds : angle 4.41979 ( 1032) SS BOND : bond 0.00541 ( 6) SS BOND : angle 0.63058 ( 12) covalent geometry : bond 0.00474 ( 7590) covalent geometry : angle 0.60743 (10318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6738 (t0) REVERT: A 132 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8237 (p90) REVERT: A 214 GLN cc_start: 0.8899 (mp10) cc_final: 0.8567 (mp10) REVERT: A 330 ARG cc_start: 0.7475 (ptp90) cc_final: 0.6330 (mpt180) REVERT: A 353 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8959 (tp) REVERT: A 398 GLU cc_start: 0.8845 (mp0) cc_final: 0.8635 (mp0) REVERT: B 95 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6745 (t0) REVERT: B 132 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8225 (p90) REVERT: B 214 GLN cc_start: 0.8905 (mp10) cc_final: 0.8578 (mp10) REVERT: B 330 ARG cc_start: 0.7466 (ptp90) cc_final: 0.6331 (mpt180) REVERT: B 353 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8936 (tp) outliers start: 23 outliers final: 5 residues processed: 107 average time/residue: 0.1751 time to fit residues: 25.9315 Evaluate side-chains 96 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110304 restraints weight = 10926.951| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.75 r_work: 0.3166 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7596 Z= 0.124 Angle : 0.530 6.210 10330 Z= 0.280 Chirality : 0.041 0.146 1252 Planarity : 0.004 0.045 1270 Dihedral : 4.388 18.092 1062 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.53 % Allowed : 13.67 % Favored : 83.80 % 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: -1.08 (0.27), residues: 1004 helix: 0.82 (0.24), residues: 546 sheet: None (None), residues: 0 loop : -2.78 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.000 HIS B 297 PHE 0.013 0.001 PHE B 132 TYR 0.010 0.001 TYR A 343 ARG 0.003 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 348) hydrogen bonds : angle 4.08474 ( 1032) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.80083 ( 12) covalent geometry : bond 0.00292 ( 7590) covalent geometry : angle 0.52940 (10318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.803 Fit side-chains REVERT: A 95 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6524 (t0) REVERT: A 132 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8095 (p90) REVERT: A 214 GLN cc_start: 0.8866 (mp10) cc_final: 0.8520 (mp10) REVERT: A 324 ILE cc_start: 0.8078 (mm) cc_final: 0.7703 (mt) REVERT: A 330 ARG cc_start: 0.7435 (ptp90) cc_final: 0.6308 (mpt180) REVERT: A 353 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8874 (tp) REVERT: B 95 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6536 (t0) REVERT: B 132 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8070 (p90) REVERT: B 324 ILE cc_start: 0.8113 (mm) cc_final: 0.7761 (mt) REVERT: B 330 ARG cc_start: 0.7437 (ptp90) cc_final: 0.6299 (mpt180) REVERT: B 353 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (tp) outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 0.1837 time to fit residues: 25.6194 Evaluate side-chains 97 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108202 restraints weight = 10806.721| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.69 r_work: 0.3133 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7596 Z= 0.161 Angle : 0.562 5.319 10330 Z= 0.296 Chirality : 0.042 0.135 1252 Planarity : 0.004 0.044 1270 Dihedral : 4.474 17.694 1062 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.91 % Allowed : 14.68 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 1004 helix: 0.79 (0.23), residues: 566 sheet: None (None), residues: 0 loop : -2.87 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.001 PHE B 132 TYR 0.009 0.001 TYR A 276 ARG 0.002 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 348) hydrogen bonds : angle 4.06213 ( 1032) SS BOND : bond 0.00042 ( 6) SS BOND : angle 0.90763 ( 12) covalent geometry : bond 0.00396 ( 7590) covalent geometry : angle 0.56149 (10318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.861 Fit side-chains REVERT: A 132 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8207 (p90) REVERT: A 214 GLN cc_start: 0.8883 (mp10) cc_final: 0.8514 (mp10) REVERT: A 330 ARG cc_start: 0.7470 (ptp90) cc_final: 0.6337 (mpt180) REVERT: A 353 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (tp) REVERT: A 398 GLU cc_start: 0.8784 (mp0) cc_final: 0.8549 (mp0) REVERT: B 132 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8193 (p90) REVERT: B 214 GLN cc_start: 0.9032 (mp10) cc_final: 0.8633 (mp10) REVERT: B 330 ARG cc_start: 0.7451 (ptp90) cc_final: 0.6322 (mpt180) REVERT: B 353 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (tp) REVERT: B 398 GLU cc_start: 0.8790 (mp0) cc_final: 0.8562 (mp0) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 0.1925 time to fit residues: 26.6894 Evaluate side-chains 94 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110917 restraints weight = 10802.550| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.73 r_work: 0.3170 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7596 Z= 0.104 Angle : 0.507 5.416 10330 Z= 0.268 Chirality : 0.041 0.271 1252 Planarity : 0.004 0.043 1270 Dihedral : 4.268 20.715 1062 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.90 % Allowed : 16.46 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 1004 helix: 0.97 (0.23), residues: 570 sheet: None (None), residues: 0 loop : -2.84 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 297 PHE 0.012 0.001 PHE B 132 TYR 0.010 0.001 TYR A 343 ARG 0.001 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 348) hydrogen bonds : angle 3.81927 ( 1032) SS BOND : bond 0.00036 ( 6) SS BOND : angle 0.71834 ( 12) covalent geometry : bond 0.00241 ( 7590) covalent geometry : angle 0.50695 (10318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.763 Fit side-chains REVERT: A 132 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8189 (p90) REVERT: A 214 GLN cc_start: 0.8889 (mp10) cc_final: 0.8525 (mp10) REVERT: A 330 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6234 (mpt180) REVERT: A 353 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 132 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8172 (p90) REVERT: B 214 GLN cc_start: 0.9002 (mp10) cc_final: 0.8601 (mp10) REVERT: B 330 ARG cc_start: 0.7359 (ptp90) cc_final: 0.6219 (mpt180) REVERT: B 353 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8866 (tp) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.1883 time to fit residues: 25.5709 Evaluate side-chains 97 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117450 restraints weight = 10280.023| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.41 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7596 Z= 0.104 Angle : 0.493 4.911 10330 Z= 0.260 Chirality : 0.040 0.228 1252 Planarity : 0.004 0.043 1270 Dihedral : 4.108 17.686 1062 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.41 % Allowed : 16.20 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1004 helix: 1.17 (0.23), residues: 570 sheet: None (None), residues: 0 loop : -2.75 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 297 PHE 0.012 0.001 PHE A 132 TYR 0.008 0.001 TYR A 343 ARG 0.001 0.000 ARG A 182 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 348) hydrogen bonds : angle 3.68829 ( 1032) SS BOND : bond 0.00063 ( 6) SS BOND : angle 0.71235 ( 12) covalent geometry : bond 0.00244 ( 7590) covalent geometry : angle 0.49305 (10318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.824 Fit side-chains REVERT: A 132 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8168 (p90) REVERT: A 214 GLN cc_start: 0.8949 (mp10) cc_final: 0.8621 (mp10) REVERT: A 330 ARG cc_start: 0.7513 (ptp90) cc_final: 0.6340 (mpt180) REVERT: A 353 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 423 SER cc_start: 0.8923 (m) cc_final: 0.8694 (t) REVERT: B 132 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8170 (p90) REVERT: B 214 GLN cc_start: 0.9039 (mp10) cc_final: 0.8683 (mp10) REVERT: B 330 ARG cc_start: 0.7493 (ptp90) cc_final: 0.6338 (mpt180) REVERT: B 353 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9013 (tp) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 0.1857 time to fit residues: 26.6102 Evaluate side-chains 99 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 0.0170 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.0770 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117938 restraints weight = 10231.440| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.38 r_work: 0.3237 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7596 Z= 0.089 Angle : 0.473 5.256 10330 Z= 0.249 Chirality : 0.040 0.215 1252 Planarity : 0.004 0.042 1270 Dihedral : 4.007 20.191 1062 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 1004 helix: 1.17 (0.23), residues: 582 sheet: None (None), residues: 0 loop : -2.59 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS B 297 PHE 0.011 0.001 PHE B 252 TYR 0.009 0.001 TYR B 343 ARG 0.002 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 348) hydrogen bonds : angle 3.55549 ( 1032) SS BOND : bond 0.00073 ( 6) SS BOND : angle 0.57839 ( 12) covalent geometry : bond 0.00202 ( 7590) covalent geometry : angle 0.47262 (10318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.828 Fit side-chains REVERT: A 132 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8197 (p90) REVERT: A 214 GLN cc_start: 0.8950 (mp10) cc_final: 0.8610 (mp10) REVERT: A 330 ARG cc_start: 0.7467 (ptp90) cc_final: 0.6358 (mpt180) REVERT: A 353 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8955 (tp) REVERT: B 132 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8194 (p90) REVERT: B 214 GLN cc_start: 0.9025 (mp10) cc_final: 0.8685 (mp10) REVERT: B 330 ARG cc_start: 0.7439 (ptp90) cc_final: 0.6335 (mpt180) REVERT: B 353 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8990 (tp) outliers start: 14 outliers final: 7 residues processed: 98 average time/residue: 0.1941 time to fit residues: 26.2290 Evaluate side-chains 94 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 61.1186 > 50: distance: 4 - 25: 15.199 distance: 9 - 36: 28.418 distance: 14 - 41: 7.033 distance: 18 - 19: 3.709 distance: 19 - 20: 9.304 distance: 19 - 25: 8.498 distance: 20 - 46: 13.296 distance: 21 - 22: 4.200 distance: 22 - 23: 9.340 distance: 22 - 24: 4.732 distance: 25 - 26: 4.815 distance: 26 - 27: 9.647 distance: 26 - 29: 6.324 distance: 27 - 28: 17.989 distance: 27 - 36: 21.011 distance: 28 - 53: 10.053 distance: 29 - 30: 3.397 distance: 30 - 31: 3.366 distance: 33 - 34: 4.472 distance: 36 - 37: 39.355 distance: 37 - 38: 10.904 distance: 37 - 40: 27.590 distance: 38 - 39: 10.691 distance: 38 - 41: 8.779 distance: 39 - 58: 12.464 distance: 41 - 42: 7.853 distance: 42 - 45: 6.754 distance: 43 - 44: 8.507 distance: 43 - 46: 4.745 distance: 44 - 65: 6.285 distance: 46 - 47: 3.642 distance: 47 - 50: 3.028 distance: 49 - 76: 6.341 distance: 50 - 51: 4.244 distance: 50 - 52: 3.226 distance: 54 - 55: 3.861 distance: 54 - 57: 6.411 distance: 55 - 56: 4.111 distance: 55 - 58: 3.701 distance: 61 - 91: 6.419 distance: 62 - 63: 6.172 distance: 62 - 64: 3.933 distance: 68 - 99: 7.711 distance: 69 - 70: 5.002 distance: 70 - 71: 3.627 distance: 71 - 73: 4.305 distance: 72 - 74: 5.683 distance: 73 - 75: 3.746 distance: 74 - 75: 3.826 distance: 77 - 78: 4.513 distance: 77 - 80: 5.244 distance: 78 - 79: 7.139 distance: 78 - 84: 4.114 distance: 81 - 82: 6.781 distance: 81 - 83: 7.324 distance: 84 - 85: 3.778 distance: 85 - 86: 3.334 distance: 85 - 88: 6.270 distance: 88 - 89: 5.707 distance: 88 - 90: 8.706