Starting phenix.real_space_refine on Wed Jun 18 08:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdm_61396/06_2025/9jdm_61396.cif" } resolution = 3.13 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= -0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 124 5.16 5 C 13824 2.51 5 N 3264 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4946 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4946 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, D Time building chain proxies: 20.51, per 1000 atoms: 0.98 Number of scatterers: 20992 At special positions: 0 Unit cell: (142.31, 142.31, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 28 15.00 O 3752 8.00 N 3264 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 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: 5.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 61.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.976A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.545A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.975A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.506A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.924A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.545A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 483 through 507 removed outlier: 4.020A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 507 " --> pdb=" O ILE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 562 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY D 678 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.976A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.546A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 562 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 606 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 667 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.976A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.700A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.646A pdb=" N ALA C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.507A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.923A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.685A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.546A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 483 through 507 removed outlier: 4.019A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 507 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.942A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 562 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 606 Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 667 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.509A pdb=" N GLY C 678 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 707 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.856A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2979 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: 5.59 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3466 1.33 - 1.45: 5433 1.45 - 1.57: 12233 1.57 - 1.69: 56 1.69 - 1.81: 204 Bond restraints: 21392 Sorted by residual: bond pdb=" CA TYR D 213 " pdb=" C TYR D 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR C 213 " pdb=" C TYR C 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" CA TYR B 213 " pdb=" C TYR B 213 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.21e-02 6.83e+03 1.12e+00 bond pdb=" C PRO B 753 " pdb=" N GLY B 754 " ideal model delta sigma weight residual 1.330 1.315 0.016 1.49e-02 4.50e+03 1.11e+00 ... (remaining 21387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 28535 2.08 - 4.16: 173 4.16 - 6.24: 20 6.24 - 8.32: 4 8.32 - 10.40: 16 Bond angle restraints: 28748 Sorted by residual: angle pdb=" C ASP C 752 " pdb=" N PRO C 753 " pdb=" CA PRO C 753 " ideal model delta sigma weight residual 120.21 113.68 6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" C ASP D 752 " pdb=" N PRO D 753 " pdb=" CA PRO D 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" C ASP A 752 " pdb=" N PRO A 753 " pdb=" CA PRO A 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" C ASP B 752 " pdb=" N PRO B 753 " pdb=" CA PRO B 753 " ideal model delta sigma weight residual 120.21 113.70 6.51 9.60e-01 1.09e+00 4.59e+01 angle pdb=" CA LEU B 711 " pdb=" CB LEU B 711 " pdb=" CG LEU B 711 " ideal model delta sigma weight residual 116.30 126.70 -10.40 3.50e+00 8.16e-02 8.83e+00 ... (remaining 28743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 11531 23.33 - 46.67: 1167 46.67 - 70.00: 247 70.00 - 93.34: 48 93.34 - 116.67: 4 Dihedral angle restraints: 12997 sinusoidal: 5821 harmonic: 7176 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.39 -52.39 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.39 -52.39 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 145.34 -52.34 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 12994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1893 0.025 - 0.050: 779 0.050 - 0.075: 371 0.075 - 0.100: 73 0.100 - 0.125: 40 Chirality restraints: 3156 Sorted by residual: chirality pdb=" C2 POV B 806 " pdb=" C1 POV B 806 " pdb=" C3 POV B 806 " pdb=" O21 POV B 806 " both_signs ideal model delta sigma weight residual False 2.43 2.30 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" C2 POV A 806 " pdb=" C1 POV A 806 " pdb=" C3 POV A 806 " pdb=" O21 POV A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.30 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 385 " pdb=" N VAL B 385 " pdb=" C VAL B 385 " pdb=" CB VAL B 385 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 3153 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 264 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 265 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 264 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 265 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 264 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 265 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.028 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 225 2.61 - 3.18: 16763 3.18 - 3.75: 32849 3.75 - 4.33: 44888 4.33 - 4.90: 75371 Nonbonded interactions: 170096 Sorted by model distance: nonbonded pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " model vdw 2.032 3.760 nonbonded pdb=" OG SER C 328 " pdb=" OD1 ASN C 330 " model vdw 2.254 3.040 nonbonded pdb=" OG SER D 328 " pdb=" OD1 ASN D 330 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 328 " pdb=" OD1 ASN A 330 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 328 " pdb=" OD1 ASN B 330 " model vdw 2.255 3.040 ... (remaining 170091 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' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or resid 802 or (resid \ 803 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P or name C210 or name C211 or name C212)) or (res \ id 804 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P )) or resid 805 or (resid \ 806 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )) or (resid 807 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C310 or name C311)))) selection = (chain 'B' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )) or resid 802 or (resid \ 803 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P or name C210 or name C211 or name C212)) or (res \ id 804 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P )) or resid 805 or (resid \ 806 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )) or (resid 807 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C310 or name C311)))) selection = (chain 'C' and (resid 119 through 755 or resid 801 or (resid 802 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216 or name C217 or name C218)) or (resid 803 and (name N or name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212)) or (resid 804 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 805 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 o \ r name C310 or name C311)) or (resid 806 and (name N or name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'D' and (resid 119 through 755 or resid 801 or (resid 802 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 or \ name C216 or name C217 or name C218)) or (resid 803 and (name N or name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212)) or (resid 804 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 805 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 o \ r name C310 or name C311)) or (resid 806 and (name N or name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) } 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: 2.090 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 52.830 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.002 0.026 21395 Z= 0.102 Angle : 0.514 10.400 28754 Z= 0.268 Chirality : 0.035 0.125 3156 Planarity : 0.003 0.051 3468 Dihedral : 19.021 116.671 8332 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -1.89 (0.15), residues: 2416 helix: -0.39 (0.12), residues: 1404 sheet: 0.57 (0.61), residues: 84 loop : -2.79 (0.16), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 742 HIS 0.004 0.001 HIS C 301 PHE 0.013 0.001 PHE D 728 TYR 0.008 0.001 TYR D 594 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.16077 ( 1005) hydrogen bonds : angle 5.94007 ( 2979) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.28930 ( 6) covalent geometry : bond 0.00197 (21392) covalent geometry : angle 0.51406 (28748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 2.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3274 time to fit residues: 162.9353 Evaluate side-chains 292 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.178530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144724 restraints weight = 24649.473| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.79 r_work: 0.3376 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21395 Z= 0.147 Angle : 0.520 8.482 28754 Z= 0.268 Chirality : 0.037 0.125 3156 Planarity : 0.004 0.052 3468 Dihedral : 14.273 117.578 3600 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.74 % Allowed : 23.05 % Favored : 74.21 % 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: -0.87 (0.16), residues: 2416 helix: 0.53 (0.13), residues: 1468 sheet: 1.28 (0.70), residues: 64 loop : -2.70 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 692 HIS 0.006 0.001 HIS D 426 PHE 0.014 0.001 PHE C 250 TYR 0.015 0.002 TYR D 451 ARG 0.002 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1005) hydrogen bonds : angle 4.24591 ( 2979) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.31328 ( 6) covalent geometry : bond 0.00343 (21392) covalent geometry : angle 0.52033 (28748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 2.316 Fit side-chains REVERT: A 574 MET cc_start: 0.8791 (mmm) cc_final: 0.8564 (mtt) REVERT: D 574 MET cc_start: 0.8799 (mmm) cc_final: 0.8578 (mtt) REVERT: B 574 MET cc_start: 0.8802 (mmm) cc_final: 0.8581 (mtt) REVERT: C 574 MET cc_start: 0.8798 (mmm) cc_final: 0.8567 (mtt) outliers start: 59 outliers final: 43 residues processed: 310 average time/residue: 0.2944 time to fit residues: 146.4456 Evaluate side-chains 290 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 691 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 160 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 134 optimal weight: 0.3980 chunk 76 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.180345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146509 restraints weight = 24527.177| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.93 r_work: 0.3390 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21395 Z= 0.100 Angle : 0.462 8.260 28754 Z= 0.236 Chirality : 0.035 0.125 3156 Planarity : 0.004 0.051 3468 Dihedral : 13.657 112.041 3600 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.70 % Allowed : 23.05 % Favored : 74.26 % 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: -0.45 (0.17), residues: 2416 helix: 0.93 (0.13), residues: 1484 sheet: 1.18 (0.67), residues: 64 loop : -2.71 (0.17), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 692 HIS 0.005 0.001 HIS D 426 PHE 0.010 0.001 PHE A 250 TYR 0.010 0.001 TYR D 594 ARG 0.001 0.000 ARG C 416 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1005) hydrogen bonds : angle 3.91347 ( 2979) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.15554 ( 6) covalent geometry : bond 0.00223 (21392) covalent geometry : angle 0.46186 (28748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7415 (t70) REVERT: A 562 MET cc_start: 0.8350 (mmm) cc_final: 0.7722 (tpp) REVERT: D 426 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7380 (t70) REVERT: D 562 MET cc_start: 0.8351 (mmm) cc_final: 0.7720 (tpp) REVERT: B 426 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7426 (t70) REVERT: B 562 MET cc_start: 0.8350 (mmm) cc_final: 0.7723 (tpp) REVERT: C 426 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7421 (t70) REVERT: C 562 MET cc_start: 0.8361 (mmm) cc_final: 0.7736 (tpp) outliers start: 58 outliers final: 37 residues processed: 315 average time/residue: 0.2940 time to fit residues: 147.5367 Evaluate side-chains 298 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 211 optimal weight: 0.0770 chunk 236 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 750 ASN C 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148514 restraints weight = 24790.377| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.89 r_work: 0.3465 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 21395 Z= 0.100 Angle : 0.465 7.779 28754 Z= 0.237 Chirality : 0.035 0.124 3156 Planarity : 0.003 0.050 3468 Dihedral : 13.319 110.900 3600 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.02 % Allowed : 22.68 % Favored : 74.30 % 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: -0.25 (0.17), residues: 2416 helix: 1.12 (0.14), residues: 1476 sheet: 1.28 (0.67), residues: 64 loop : -2.65 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 692 HIS 0.006 0.001 HIS D 160 PHE 0.009 0.001 PHE C 538 TYR 0.010 0.001 TYR A 451 ARG 0.001 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 1005) hydrogen bonds : angle 3.80915 ( 2979) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.12344 ( 6) covalent geometry : bond 0.00224 (21392) covalent geometry : angle 0.46470 (28748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (t70) REVERT: A 562 MET cc_start: 0.8529 (mmm) cc_final: 0.7930 (tpp) REVERT: D 426 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7610 (t70) REVERT: D 562 MET cc_start: 0.8559 (mmm) cc_final: 0.7966 (tpp) REVERT: B 426 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7655 (t70) REVERT: B 562 MET cc_start: 0.8557 (mmm) cc_final: 0.7964 (tpp) REVERT: C 426 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7597 (t70) REVERT: C 562 MET cc_start: 0.8544 (mmm) cc_final: 0.7944 (tpp) outliers start: 65 outliers final: 46 residues processed: 333 average time/residue: 0.2964 time to fit residues: 156.7506 Evaluate side-chains 312 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 60.7373 > 50: distance: 12 - 26: 5.626 distance: 16 - 34: 18.306 distance: 23 - 26: 6.407 distance: 27 - 28: 16.054 distance: 27 - 30: 6.916 distance: 28 - 29: 17.996 distance: 28 - 34: 16.284 distance: 30 - 31: 6.615 distance: 30 - 32: 4.936 distance: 31 - 33: 10.824 distance: 34 - 35: 28.113 distance: 35 - 36: 21.569 distance: 35 - 38: 22.943 distance: 36 - 37: 22.726 distance: 36 - 45: 41.259 distance: 38 - 39: 25.247 distance: 39 - 40: 18.892 distance: 39 - 41: 13.718 distance: 40 - 42: 16.822 distance: 41 - 43: 16.177 distance: 42 - 44: 8.072 distance: 43 - 44: 6.863 distance: 45 - 46: 22.310 distance: 46 - 47: 14.274 distance: 46 - 49: 26.166 distance: 47 - 48: 36.826 distance: 47 - 53: 45.031 distance: 49 - 50: 37.272 distance: 50 - 51: 35.196 distance: 50 - 52: 36.848 distance: 53 - 54: 24.349 distance: 54 - 55: 23.392 distance: 54 - 57: 20.417 distance: 55 - 56: 45.019 distance: 55 - 61: 30.170 distance: 57 - 58: 20.445 distance: 58 - 59: 22.196 distance: 58 - 60: 13.475 distance: 61 - 62: 21.959 distance: 62 - 63: 32.473 distance: 62 - 65: 22.204 distance: 63 - 64: 17.763 distance: 63 - 72: 36.871 distance: 65 - 66: 28.400 distance: 66 - 67: 21.659 distance: 67 - 68: 9.478 distance: 68 - 69: 5.258 distance: 69 - 70: 6.279 distance: 69 - 71: 4.695 distance: 72 - 73: 26.370 distance: 72 - 78: 23.605 distance: 73 - 74: 48.662 distance: 73 - 76: 20.680 distance: 74 - 75: 42.281 distance: 74 - 79: 29.360 distance: 76 - 77: 5.165 distance: 77 - 78: 15.152 distance: 79 - 80: 12.618 distance: 80 - 81: 13.787 distance: 80 - 83: 18.057 distance: 81 - 82: 12.445 distance: 81 - 85: 24.690 distance: 83 - 84: 20.645 distance: 85 - 86: 14.647 distance: 86 - 87: 20.543 distance: 86 - 89: 15.071 distance: 87 - 88: 17.472 distance: 87 - 93: 29.688 distance: 89 - 90: 16.786 distance: 90 - 91: 10.873 distance: 90 - 92: 17.204 distance: 93 - 94: 22.762 distance: 94 - 95: 27.354 distance: 94 - 97: 33.029 distance: 95 - 96: 27.433 distance: 95 - 101: 30.949 distance: 97 - 98: 33.472 distance: 98 - 99: 22.333 distance: 98 - 100: 37.621 distance: 101 - 102: 8.313 distance: 102 - 103: 17.518 distance: 102 - 105: 37.755 distance: 103 - 104: 5.953 distance: 103 - 110: 11.204 distance: 105 - 106: 17.135 distance: 106 - 107: 7.798 distance: 107 - 108: 3.532