Starting phenix.real_space_refine on Thu Jan 16 03:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.map" model { file = "/net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0z_14435/01_2025/7z0z_14435.cif" } resolution = 2.68 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= 0.004 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 29130 atoms to isotropic. 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 114 5.16 5 C 19122 2.51 5 N 4722 2.21 5 O 5508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 29466 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4911 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.53, per 1000 atoms: 0.29 Number of scatterers: 29466 At special positions: 0 Unit cell: (163.18, 147.6, 115.62, 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 114 16.00 O 5508 8.00 N 4722 7.00 C 19122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 64.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 0 through 13 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 402 Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'B' and resid 1 through 13 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 534 through 545 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'C' and resid 1 through 13 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.828A pdb=" N SER C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.856A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 273 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 310 through 331 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.687A pdb=" N ASP C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 402 Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 504 removed outlier: 3.537A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 517 through 530 Processing helix chain 'C' and resid 534 through 545 Processing helix chain 'C' and resid 559 through 564 Processing helix chain 'C' and resid 570 through 582 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 217 through 238 removed outlier: 3.529A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 273 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR D 282 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 310 through 331 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 Processing helix chain 'D' and resid 404 through 419 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 517 through 530 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 570 through 582 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.827A pdb=" N SER E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.198A pdb=" N TRP E 178 " --> pdb=" O HIS E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG E 221 " --> pdb=" O ASN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 273 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR E 282 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 310 through 331 Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 419 Processing helix chain 'E' and resid 419 through 434 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 504 removed outlier: 3.538A pdb=" N LYS E 494 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 517 through 530 Processing helix chain 'E' and resid 534 through 545 Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 570 through 582 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.826A pdb=" N SER F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.857A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.199A pdb=" N TRP F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 217 through 238 removed outlier: 3.528A pdb=" N ARG F 221 " --> pdb=" O ASN F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 273 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.612A pdb=" N THR F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 310 through 331 Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 372 through 384 removed outlier: 3.688A pdb=" N ASP F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 402 Processing helix chain 'F' and resid 404 through 419 Processing helix chain 'F' and resid 419 through 434 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 462 through 464 No H-bonds generated for 'chain 'F' and resid 462 through 464' Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.673A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 504 removed outlier: 3.536A pdb=" N LYS F 494 " --> pdb=" O LYS F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 517 through 530 Processing helix chain 'F' and resid 534 through 545 Processing helix chain 'F' and resid 559 through 564 Processing helix chain 'F' and resid 570 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 245 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 89 Processing sheet with id=AA6, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AA7, first strand: chain 'D' and resid 84 through 89 Processing sheet with id=AA8, first strand: chain 'D' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 243 through 245 Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 89 Processing sheet with id=AB3, first strand: chain 'F' and resid 243 through 245 1567 hydrogen bonds defined for protein. 4485 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: 7.89 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4865 1.31 - 1.43: 8737 1.43 - 1.56: 16404 1.56 - 1.68: 0 1.68 - 1.81: 174 Bond restraints: 30180 Sorted by residual: bond pdb=" C TYR D 245 " pdb=" O TYR D 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C TYR F 245 " pdb=" O TYR F 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.81e+01 bond pdb=" C TYR A 245 " pdb=" O TYR A 245 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" C TYR C 245 " pdb=" O TYR C 245 " ideal model delta sigma weight residual 1.236 1.186 0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C TYR E 245 " pdb=" O TYR E 245 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.17e-02 7.31e+03 1.76e+01 ... (remaining 30175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 40142 2.37 - 4.75: 429 4.75 - 7.12: 79 7.12 - 9.49: 6 9.49 - 11.87: 12 Bond angle restraints: 40668 Sorted by residual: angle pdb=" N GLU B 489 " pdb=" CA GLU B 489 " pdb=" C GLU B 489 " ideal model delta sigma weight residual 114.56 102.69 11.87 1.27e+00 6.20e-01 8.73e+01 angle pdb=" N GLU A 489 " pdb=" CA GLU A 489 " pdb=" C GLU A 489 " ideal model delta sigma weight residual 114.56 102.70 11.86 1.27e+00 6.20e-01 8.72e+01 angle pdb=" N GLU E 489 " pdb=" CA GLU E 489 " pdb=" C GLU E 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.71e+01 angle pdb=" N GLU C 489 " pdb=" CA GLU C 489 " pdb=" C GLU C 489 " ideal model delta sigma weight residual 114.56 102.71 11.85 1.27e+00 6.20e-01 8.70e+01 angle pdb=" N GLU D 489 " pdb=" CA GLU D 489 " pdb=" C GLU D 489 " ideal model delta sigma weight residual 114.56 102.72 11.84 1.27e+00 6.20e-01 8.69e+01 ... (remaining 40663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16137 18.02 - 36.04: 1404 36.04 - 54.06: 246 54.06 - 72.08: 63 72.08 - 90.10: 54 Dihedral angle restraints: 17904 sinusoidal: 7398 harmonic: 10506 Sorted by residual: dihedral pdb=" C VAL A 246 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL F 246 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta harmonic sigma weight residual -122.00 -135.85 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C VAL E 246 " pdb=" N VAL E 246 " pdb=" CA VAL E 246 " pdb=" CB VAL E 246 " ideal model delta harmonic sigma weight residual -122.00 -135.84 13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3829 0.078 - 0.155: 429 0.155 - 0.233: 32 0.233 - 0.311: 6 0.311 - 0.389: 6 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA VAL E 246 " pdb=" N VAL E 246 " pdb=" C VAL E 246 " pdb=" CB VAL E 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 246 " pdb=" N VAL B 246 " pdb=" C VAL B 246 " pdb=" CB VAL B 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL F 246 " pdb=" N VAL F 246 " pdb=" C VAL F 246 " pdb=" CB VAL F 246 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 4299 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA D 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA D 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER D 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 185 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA E 185 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA E 185 " 0.027 2.00e-02 2.50e+03 pdb=" N SER E 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 185 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA A 185 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA A 185 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 186 " -0.024 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 28315 3.22 - 3.78: 47268 3.78 - 4.34: 70523 4.34 - 4.90: 112653 Nonbonded interactions: 259131 Sorted by model distance: nonbonded pdb=" OH TYR E 522 " pdb=" O VAL E 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR F 522 " pdb=" O VAL F 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR C 522 " pdb=" O VAL C 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 522 " pdb=" O VAL A 584 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR D 522 " pdb=" O VAL D 584 " model vdw 2.092 3.040 ... (remaining 259126 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.730 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.072 30180 Z= 0.378 Angle : 0.718 11.868 40668 Z= 0.446 Chirality : 0.053 0.389 4302 Planarity : 0.004 0.041 5190 Dihedral : 14.672 90.096 11112 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.87 % Favored : 97.96 % Rotamer: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.91 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 9.09 % 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 (0.14), residues: 3474 helix: 0.82 (0.11), residues: 2124 sheet: 0.80 (0.41), residues: 156 loop : -0.59 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 585 HIS 0.005 0.001 HIS D 67 PHE 0.026 0.002 PHE E 44 TYR 0.029 0.002 TYR E 106 ARG 0.003 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 558 time to evaluate : 2.626 Fit side-chains REVERT: A 208 ASP cc_start: 0.8174 (m-30) cc_final: 0.7971 (m-30) REVERT: B 3 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8247 (tttm) REVERT: B 488 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 548 ASN cc_start: 0.7717 (t0) cc_final: 0.7493 (t0) REVERT: C 228 MET cc_start: 0.8932 (mmp) cc_final: 0.8717 (mmp) REVERT: C 280 ASN cc_start: 0.7940 (m110) cc_final: 0.7586 (m-40) REVERT: C 488 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 248 ASP cc_start: 0.6629 (t0) cc_final: 0.6427 (t0) REVERT: D 280 ASN cc_start: 0.7774 (m110) cc_final: 0.7506 (m110) REVERT: E 21 TYR cc_start: 0.8994 (m-80) cc_final: 0.8701 (m-80) REVERT: E 488 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (mt) REVERT: F 3 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8353 (tttm) REVERT: F 488 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7755 (mt) REVERT: F 548 ASN cc_start: 0.7705 (t0) cc_final: 0.7496 (t0) outliers start: 18 outliers final: 2 residues processed: 561 average time/residue: 1.2875 time to fit residues: 832.1479 Evaluate side-chains 400 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 394 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 537 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 389 ASN A 399 ASN A 433 ASN A 436 ASN A 505 ASN B 30 ASN B 399 ASN B 433 ASN B 436 ASN C 30 ASN C 87 ASN C 389 ASN C 399 ASN C 433 ASN C 436 ASN C 548 ASN D 30 ASN D 87 ASN D 280 ASN D 286 ASN D 389 ASN D 399 ASN D 433 ASN D 436 ASN D 543 GLN D 548 ASN E 30 ASN E 87 ASN E 110 ASN E 399 ASN E 433 ASN E 436 ASN F 30 ASN F 67 HIS F 110 ASN F 399 ASN F 433 ASN F 436 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100741 restraints weight = 36957.064| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.82 r_work: 0.3016 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30180 Z= 0.205 Angle : 0.486 5.731 40668 Z= 0.270 Chirality : 0.041 0.148 4302 Planarity : 0.003 0.043 5190 Dihedral : 4.555 39.312 3812 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.38 % Favored : 98.45 % Rotamer: Outliers : 1.30 % Allowed : 8.71 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.81 (0.15), residues: 3474 helix: 1.17 (0.11), residues: 2166 sheet: 0.66 (0.44), residues: 156 loop : -0.61 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 585 HIS 0.005 0.001 HIS F 67 PHE 0.016 0.002 PHE D 231 TYR 0.018 0.002 TYR C 525 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 451 time to evaluate : 2.640 Fit side-chains REVERT: A 29 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7281 (mmtt) REVERT: A 488 LEU cc_start: 0.8354 (mt) cc_final: 0.8117 (pp) REVERT: A 568 LYS cc_start: 0.8869 (ptmm) cc_final: 0.8225 (pmtt) REVERT: B 3 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8416 (tttm) REVERT: B 233 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8431 (tttt) REVERT: B 537 GLU cc_start: 0.6582 (tp30) cc_final: 0.6342 (tp30) REVERT: B 548 ASN cc_start: 0.7893 (t0) cc_final: 0.7645 (t0) REVERT: B 568 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8336 (pmtt) REVERT: B 591 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: C 2 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7126 (mptm) REVERT: C 29 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7641 (tptt) REVERT: C 280 ASN cc_start: 0.8289 (m110) cc_final: 0.8007 (m-40) REVERT: D 29 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7498 (mmpt) REVERT: D 146 GLN cc_start: 0.8362 (mm110) cc_final: 0.8028 (mm-40) REVERT: D 568 LYS cc_start: 0.8785 (ptmm) cc_final: 0.8205 (pmtt) REVERT: E 21 TYR cc_start: 0.9261 (m-80) cc_final: 0.8986 (m-80) REVERT: E 29 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7668 (mmpt) REVERT: F 3 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8427 (tttm) REVERT: F 29 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7383 (mmtt) REVERT: F 356 LYS cc_start: 0.8367 (mppt) cc_final: 0.8070 (mppt) REVERT: F 360 ASN cc_start: 0.8322 (t0) cc_final: 0.8068 (t0) REVERT: F 537 GLU cc_start: 0.6575 (tp30) cc_final: 0.6330 (tp30) REVERT: F 548 ASN cc_start: 0.7849 (t0) cc_final: 0.7632 (t0) REVERT: F 568 LYS cc_start: 0.8975 (ptmm) cc_final: 0.8277 (pmtt) outliers start: 43 outliers final: 13 residues processed: 470 average time/residue: 1.1997 time to fit residues: 656.9298 Evaluate side-chains 413 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 395 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 236 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 199 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 92 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 344 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 110 ASN A 217 ASN B 30 ASN B 217 ASN B 311 ASN B 360 ASN B 543 GLN C 30 ASN C 110 ASN C 217 ASN C 311 ASN C 548 ASN D 30 ASN D 110 ASN D 217 ASN D 311 ASN D 389 ASN D 548 ASN E 30 ASN E 110 ASN E 280 ASN E 311 ASN E 360 ASN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 543 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099913 restraints weight = 36857.233| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.81 r_work: 0.3000 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30180 Z= 0.202 Angle : 0.457 5.488 40668 Z= 0.253 Chirality : 0.041 0.146 4302 Planarity : 0.003 0.041 5190 Dihedral : 4.178 22.968 3798 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.55 % Favored : 98.27 % Rotamer: Outliers : 1.60 % Allowed : 9.68 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.99 (0.15), residues: 3474 helix: 1.36 (0.11), residues: 2178 sheet: 0.33 (0.43), residues: 156 loop : -0.60 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 585 HIS 0.004 0.001 HIS D 230 PHE 0.014 0.001 PHE D 231 TYR 0.012 0.001 TYR B 227 ARG 0.003 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 423 time to evaluate : 2.650 Fit side-chains REVERT: A 29 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7621 (mmpt) REVERT: A 543 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: A 568 LYS cc_start: 0.8889 (ptmm) cc_final: 0.8242 (pmtt) REVERT: B 3 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8436 (tttm) REVERT: B 29 LYS cc_start: 0.7875 (tmtt) cc_final: 0.7649 (mmpt) REVERT: B 233 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8442 (ttpp) REVERT: B 548 ASN cc_start: 0.7892 (t0) cc_final: 0.7635 (t0) REVERT: B 568 LYS cc_start: 0.8926 (ptmm) cc_final: 0.8381 (pmtt) REVERT: B 591 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: C 2 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7196 (mptm) REVERT: C 29 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7666 (tptt) REVERT: C 356 LYS cc_start: 0.8221 (mppt) cc_final: 0.7759 (mmtm) REVERT: D 4 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7846 (mp0) REVERT: D 29 LYS cc_start: 0.7935 (tmtt) cc_final: 0.7507 (mmpt) REVERT: D 93 GLU cc_start: 0.7479 (pm20) cc_final: 0.7016 (pp20) REVERT: D 146 GLN cc_start: 0.8391 (mm110) cc_final: 0.8065 (mm-40) REVERT: D 568 LYS cc_start: 0.8779 (ptmm) cc_final: 0.8192 (pmtt) REVERT: E 29 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7710 (mmpt) REVERT: F 1 MET cc_start: 0.7883 (ttm) cc_final: 0.7409 (ttm) REVERT: F 4 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7573 (mp0) REVERT: F 29 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7693 (mmpt) REVERT: F 356 LYS cc_start: 0.8407 (mppt) cc_final: 0.8133 (mptt) REVERT: F 548 ASN cc_start: 0.7817 (t0) cc_final: 0.7584 (t0) REVERT: F 568 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8249 (pmtt) outliers start: 53 outliers final: 14 residues processed: 451 average time/residue: 1.1778 time to fit residues: 620.0579 Evaluate side-chains 403 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 383 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 271 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 110 ASN A 217 ASN A 311 ASN B 30 ASN B 110 ASN B 543 GLN C 30 ASN C 110 ASN C 548 ASN D 30 ASN D 110 ASN D 217 ASN D 280 ASN D 548 ASN E 110 ASN E 280 ASN E 548 ASN F 30 ASN F 67 HIS F 110 ASN F 217 ASN F 311 ASN F 543 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095614 restraints weight = 37384.688| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.80 r_work: 0.2965 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30180 Z= 0.381 Angle : 0.527 7.848 40668 Z= 0.289 Chirality : 0.044 0.153 4302 Planarity : 0.003 0.045 5190 Dihedral : 4.360 25.861 3798 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 2.36 % Allowed : 9.59 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.84 (0.14), residues: 3474 helix: 1.23 (0.11), residues: 2172 sheet: 0.11 (0.42), residues: 156 loop : -0.57 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 585 HIS 0.006 0.001 HIS D 230 PHE 0.018 0.002 PHE C 231 TYR 0.014 0.002 TYR D 227 ARG 0.004 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 403 time to evaluate : 2.656 Fit side-chains REVERT: A 29 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7687 (mmpt) REVERT: A 276 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 543 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: B 1 MET cc_start: 0.7972 (ttm) cc_final: 0.7621 (ttm) REVERT: B 29 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7713 (mmpt) REVERT: B 356 LYS cc_start: 0.8362 (mppt) cc_final: 0.8030 (mptt) REVERT: B 431 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8621 (mtp-110) REVERT: B 548 ASN cc_start: 0.7895 (t0) cc_final: 0.7607 (t0) REVERT: B 568 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8356 (pmtt) REVERT: C 2 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7167 (mptm) REVERT: C 4 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7805 (mp0) REVERT: C 29 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (tptt) REVERT: C 579 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8352 (mp) REVERT: D 4 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7857 (mp0) REVERT: D 93 GLU cc_start: 0.7538 (pm20) cc_final: 0.7169 (pp20) REVERT: D 146 GLN cc_start: 0.8426 (mm110) cc_final: 0.8071 (mm-40) REVERT: D 568 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8233 (pmtt) REVERT: E 4 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: E 334 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8125 (mmpt) REVERT: E 591 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: F 4 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7673 (mp0) REVERT: F 356 LYS cc_start: 0.8414 (mppt) cc_final: 0.8080 (mppt) REVERT: F 431 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8647 (mtp-110) REVERT: F 490 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8472 (mtmt) REVERT: F 548 ASN cc_start: 0.7845 (t0) cc_final: 0.7639 (t0) REVERT: F 568 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8223 (pmtt) REVERT: F 591 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6769 (mp0) outliers start: 78 outliers final: 21 residues processed: 444 average time/residue: 1.2497 time to fit residues: 641.8393 Evaluate side-chains 415 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 334 LYS Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 490 LYS Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 591 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 3 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 234 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 257 ASN A 548 ASN B 217 ASN C 30 ASN C 217 ASN C 260 GLN C 548 ASN D 30 ASN D 280 ASN D 548 ASN E 217 ASN E 548 ASN F 67 HIS F 260 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098821 restraints weight = 36810.539| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.84 r_work: 0.2984 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30180 Z= 0.188 Angle : 0.451 6.322 40668 Z= 0.248 Chirality : 0.040 0.148 4302 Planarity : 0.003 0.040 5190 Dihedral : 4.129 24.263 3798 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.76 % Favored : 98.07 % Rotamer: Outliers : 1.94 % Allowed : 10.98 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.05 (0.15), residues: 3474 helix: 1.45 (0.11), residues: 2178 sheet: 0.02 (0.41), residues: 156 loop : -0.62 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 585 HIS 0.003 0.001 HIS D 230 PHE 0.014 0.001 PHE E 231 TYR 0.014 0.001 TYR C 227 ARG 0.002 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 405 time to evaluate : 2.644 Fit side-chains REVERT: A 29 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7690 (mmpt) REVERT: A 96 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8514 (ttp-110) REVERT: A 543 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: A 568 LYS cc_start: 0.8843 (ptmm) cc_final: 0.8248 (pmtt) REVERT: B 29 LYS cc_start: 0.7935 (tmtt) cc_final: 0.7685 (mmpt) REVERT: B 169 HIS cc_start: 0.8199 (m-70) cc_final: 0.7993 (m-70) REVERT: B 356 LYS cc_start: 0.8353 (mppt) cc_final: 0.8080 (mptt) REVERT: B 548 ASN cc_start: 0.7907 (t0) cc_final: 0.7696 (t0) REVERT: B 568 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8370 (pmtt) REVERT: C 2 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7213 (mptm) REVERT: C 29 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7623 (mmpt) REVERT: C 579 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 591 GLU cc_start: 0.7551 (pt0) cc_final: 0.7223 (mp0) REVERT: D 4 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7924 (mp0) REVERT: D 29 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7571 (mmpt) REVERT: D 93 GLU cc_start: 0.7527 (pm20) cc_final: 0.7173 (pp20) REVERT: D 146 GLN cc_start: 0.8398 (mm110) cc_final: 0.8040 (mm-40) REVERT: D 257 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8031 (p0) REVERT: D 568 LYS cc_start: 0.8815 (ptmm) cc_final: 0.8243 (pmtt) REVERT: D 591 GLU cc_start: 0.7745 (pt0) cc_final: 0.7309 (mp0) REVERT: E 4 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: E 334 LYS cc_start: 0.8511 (mtmp) cc_final: 0.8150 (mmpt) REVERT: F 1 MET cc_start: 0.8012 (ttm) cc_final: 0.7744 (ttm) REVERT: F 4 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7657 (mp0) REVERT: F 29 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7689 (mmpt) REVERT: F 146 GLN cc_start: 0.8211 (mm110) cc_final: 0.7798 (mm-40) REVERT: F 169 HIS cc_start: 0.8195 (m-70) cc_final: 0.7984 (m-70) REVERT: F 356 LYS cc_start: 0.8418 (mppt) cc_final: 0.8132 (mptt) REVERT: F 548 ASN cc_start: 0.7852 (t0) cc_final: 0.7600 (t0) REVERT: F 568 LYS cc_start: 0.8937 (ptmm) cc_final: 0.8333 (pmtt) REVERT: F 591 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6782 (mp0) outliers start: 64 outliers final: 23 residues processed: 432 average time/residue: 1.1782 time to fit residues: 593.9065 Evaluate side-chains 416 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain F residue 593 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2747 > 50: distance: 68 - 72: 7.205 distance: 72 - 73: 15.061 distance: 73 - 74: 19.455 distance: 73 - 76: 9.267 distance: 74 - 75: 38.929 distance: 74 - 83: 27.557 distance: 76 - 77: 6.447 distance: 77 - 78: 6.107 distance: 77 - 79: 9.201 distance: 78 - 80: 11.731 distance: 79 - 81: 9.899 distance: 80 - 82: 8.928 distance: 81 - 82: 10.649 distance: 83 - 84: 7.896 distance: 84 - 85: 17.476 distance: 84 - 87: 11.387 distance: 85 - 86: 9.898 distance: 85 - 91: 14.987 distance: 86 - 119: 7.492 distance: 87 - 88: 5.360 distance: 88 - 89: 15.126 distance: 88 - 90: 5.857 distance: 91 - 92: 11.190 distance: 92 - 93: 8.824 distance: 92 - 95: 14.138 distance: 93 - 94: 15.948 distance: 93 - 103: 16.095 distance: 94 - 126: 11.043 distance: 95 - 96: 6.899 distance: 96 - 97: 5.656 distance: 96 - 98: 3.997 distance: 97 - 99: 6.389 distance: 99 - 101: 5.071 distance: 100 - 101: 4.360 distance: 101 - 102: 11.102 distance: 103 - 104: 10.391 distance: 103 - 109: 4.415 distance: 104 - 105: 7.190 distance: 104 - 107: 10.102 distance: 105 - 110: 5.693 distance: 106 - 135: 7.279 distance: 107 - 108: 4.323 distance: 108 - 109: 12.526 distance: 111 - 112: 5.084 distance: 111 - 114: 9.546 distance: 112 - 119: 4.292 distance: 113 - 144: 12.198 distance: 114 - 115: 10.107 distance: 115 - 116: 14.493 distance: 116 - 117: 5.809 distance: 117 - 118: 3.633 distance: 119 - 120: 5.385 distance: 120 - 121: 5.312 distance: 120 - 123: 9.431 distance: 121 - 122: 6.184 distance: 121 - 126: 10.196 distance: 122 - 152: 10.534 distance: 123 - 124: 4.150 distance: 123 - 125: 10.477 distance: 126 - 127: 4.181 distance: 127 - 128: 10.601 distance: 127 - 130: 9.553 distance: 128 - 129: 13.679 distance: 128 - 135: 5.032 distance: 129 - 159: 11.614 distance: 130 - 131: 4.016 distance: 131 - 132: 14.247 distance: 132 - 134: 4.827 distance: 135 - 136: 5.057 distance: 136 - 137: 8.024 distance: 136 - 139: 5.287 distance: 137 - 138: 3.996 distance: 137 - 144: 6.614 distance: 138 - 168: 8.851 distance: 139 - 140: 9.078 distance: 140 - 141: 6.413 distance: 141 - 142: 4.339 distance: 141 - 143: 20.133 distance: 144 - 145: 8.577 distance: 145 - 146: 10.013 distance: 145 - 148: 3.222 distance: 146 - 147: 10.420 distance: 146 - 152: 6.368 distance: 147 - 174: 9.501 distance: 148 - 149: 5.881 distance: 148 - 150: 12.708 distance: 149 - 151: 12.279 distance: 152 - 153: 5.589 distance: 154 - 159: 3.651 distance: 155 - 181: 5.846 distance: 156 - 157: 6.150 distance: 156 - 158: 5.168