Starting phenix.real_space_refine on Fri Jun 13 23:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840.map" model { file = "/net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi5_23840/06_2025/7mi5_23840_neut.cif" } resolution = 3.57 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= 0.049 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: 7 Type Number sf(0) Gaussians Mn 6 7.51 5 Fe 4 7.16 5 P 60 5.49 5 S 87 5.16 5 C 9573 2.51 5 N 2847 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15469 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4347 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 35, 'TRANS': 517} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2887 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 22, 'TRANS': 339} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 134 SG CYS A 22 58.998 39.159 120.263 1.00121.43 S ATOM 1460 SG CYS A 196 60.316 44.706 121.026 1.00115.75 S ATOM 1421 SG CYS A 190 56.911 44.316 116.691 1.00122.55 S ATOM 1397 SG CYS A 187 61.613 42.265 116.734 1.00110.23 S Restraints were copied for chains: D, F Time building chain proxies: 10.58, per 1000 atoms: 0.68 Number of scatterers: 15469 At special positions: 0 Unit cell: (94.71, 105.78, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Mn 6 24.99 S 87 16.00 P 60 15.00 O 2892 8.00 N 2847 7.00 C 9573 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: 4.31 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " Number of angles added : 12 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 18 sheets defined 51.0% alpha, 12.9% beta 16 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.509A pdb=" N TYR A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.693A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 4.226A pdb=" N ALA A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 155 through 175 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.599A pdb=" N ARG A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 353 through 369 removed outlier: 3.611A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.241A pdb=" N SER A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 7.180A pdb=" N ARG A 396 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.566A pdb=" N ARG A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 441 removed outlier: 3.867A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.968A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 483 removed outlier: 4.664A pdb=" N LEU A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.654A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 removed outlier: 3.536A pdb=" N CYS B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 removed outlier: 3.788A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 392 removed outlier: 3.815A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 417 through 441 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.689A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.628A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 316 through 343 Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.610A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 392 removed outlier: 4.240A pdb=" N SER C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 removed outlier: 7.180A pdb=" N ARG C 396 " --> pdb=" O ARG C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.567A pdb=" N ARG C 410 " --> pdb=" O PHE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 441 removed outlier: 3.867A pdb=" N GLU C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.967A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 483 removed outlier: 4.664A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 489 No H-bonds generated for 'chain 'C' and resid 487 through 489' Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 301 through 316 removed outlier: 3.653A pdb=" N GLU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 removed outlier: 3.535A pdb=" N CYS D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 370 removed outlier: 3.787A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 370 " --> pdb=" O HIS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 392 removed outlier: 3.814A pdb=" N HIS D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 417 through 441 Processing helix chain 'D' and resid 458 through 466 removed outlier: 3.688A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing helix chain 'D' and resid 501 through 518 Processing helix chain 'D' and resid 531 through 546 removed outlier: 3.629A pdb=" N GLU D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'E' and resid 13 through 26 Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'F' and resid 13 through 26 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.047A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 73 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.912A pdb=" N VAL A 96 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA A 139 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 141 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 100 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.771A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N THR A 284 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 260 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 286 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 262 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A 283 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 297 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 295 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR B 284 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 222 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN B 259 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 253 removed outlier: 5.401A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 removed outlier: 3.604A pdb=" N ALA B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.771A pdb=" N LEU C 222 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA C 261 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 224 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 263 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 226 " --> pdb=" O PHE C 263 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N THR C 284 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 260 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU C 286 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 262 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 283 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL C 297 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS D 295 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 294 " --> pdb=" O TRP D 285 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR D 284 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU D 286 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU D 262 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 222 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN D 259 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 253 removed outlier: 5.401A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 244 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 251 removed outlier: 3.603A pdb=" N ALA D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 491 through 493 Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 520 Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.486A pdb=" N VAL E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 69 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 6 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP E 67 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER E 8 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE E 65 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP E 10 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 63 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 78 through 80 removed outlier: 5.162A pdb=" N VAL F 63 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP F 10 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE F 65 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER F 8 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP F 67 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE F 6 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY F 69 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) 733 hydrogen bonds defined for protein. 2115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 6894 1.42 - 1.63: 8898 1.63 - 1.85: 137 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 15941 Sorted by residual: bond pdb=" C1' DG H 20 " pdb=" N9 DG H 20 " ideal model delta sigma weight residual 1.460 1.360 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1' DA H 21 " pdb=" N9 DA H 21 " ideal model delta sigma weight residual 1.460 1.368 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" SD MET D 364 " pdb=" CE MET D 364 " ideal model delta sigma weight residual 1.791 1.695 0.096 2.50e-02 1.60e+03 1.46e+01 bond pdb=" SD MET B 364 " pdb=" CE MET B 364 " ideal model delta sigma weight residual 1.791 1.696 0.095 2.50e-02 1.60e+03 1.44e+01 bond pdb=" C LEU A 197 " pdb=" O LEU A 197 " ideal model delta sigma weight residual 1.233 1.250 -0.017 4.80e-03 4.34e+04 1.29e+01 ... (remaining 15936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.40: 21697 6.40 - 12.80: 112 12.80 - 19.20: 17 19.20 - 25.60: 5 25.60 - 32.00: 4 Bond angle restraints: 21835 Sorted by residual: angle pdb=" CA MET D 364 " pdb=" CB MET D 364 " pdb=" CG MET D 364 " ideal model delta sigma weight residual 114.10 139.65 -25.55 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET B 364 " pdb=" CB MET B 364 " pdb=" CG MET B 364 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET D 479 " pdb=" CB MET D 479 " pdb=" CG MET D 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CA MET B 479 " pdb=" CB MET B 479 " pdb=" CG MET B 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CB MET B 479 " pdb=" CG MET B 479 " pdb=" SD MET B 479 " ideal model delta sigma weight residual 112.70 144.70 -32.00 3.00e+00 1.11e-01 1.14e+02 ... (remaining 21830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 8506 29.22 - 58.43: 797 58.43 - 87.65: 103 87.65 - 116.87: 4 116.87 - 146.08: 2 Dihedral angle restraints: 9412 sinusoidal: 4289 harmonic: 5123 Sorted by residual: dihedral pdb=" CA ARG B 412 " pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N ARG D 413 " pdb=" CA ARG D 413 " ideal model delta harmonic sigma weight residual -180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA GLN C 312 " pdb=" C GLN C 312 " pdb=" N ARG C 313 " pdb=" CA ARG C 313 " ideal model delta harmonic sigma weight residual 180.00 149.32 30.68 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2013 0.084 - 0.169: 293 0.169 - 0.253: 47 0.253 - 0.338: 6 0.338 - 0.422: 2 Chirality restraints: 2361 Sorted by residual: chirality pdb=" CA MET B 364 " pdb=" N MET B 364 " pdb=" C MET B 364 " pdb=" CB MET B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET D 364 " pdb=" N MET D 364 " pdb=" C MET D 364 " pdb=" CB MET D 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR A 232 " pdb=" N TYR A 232 " pdb=" C TYR A 232 " pdb=" CB TYR A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2358 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 327 " 0.029 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP D 327 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 327 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP D 327 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 327 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 327 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 327 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 327 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 327 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 327 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 327 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B 327 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 327 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 327 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 327 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 327 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 327 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 327 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 340 " 0.061 9.50e-02 1.11e+02 3.44e-02 5.96e+00 pdb=" NE ARG B 340 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 340 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 340 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 124 2.31 - 2.96: 8814 2.96 - 3.60: 25515 3.60 - 4.25: 38226 4.25 - 4.90: 60951 Nonbonded interactions: 133630 Sorted by model distance: nonbonded pdb=" N2 DG G 8 " pdb=" N3 DG H 20 " model vdw 1.662 3.200 nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.716 2.320 nonbonded pdb=" N GLY A 237 " pdb=" OP1 DT G 6 " model vdw 1.916 3.120 nonbonded pdb=" NE2 HIS A 48 " pdb="MN MN H 801 " model vdw 1.916 2.400 nonbonded pdb=" C2 DG G 8 " pdb=" C2 DG H 20 " model vdw 1.925 3.480 ... (remaining 133625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 219 through 558) selection = (chain 'C' and resid 219 through 558) selection = (chain 'D' and resid 219 through 558) } ncs_group { reference = chain 'E' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 45.030 Find NCS groups from input model: 0.500 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 : 0.010 0.362 15945 Z= 0.471 Angle : 1.605 60.520 21847 Z= 0.789 Chirality : 0.063 0.422 2361 Planarity : 0.006 0.045 2644 Dihedral : 21.219 146.085 6130 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 35.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 11.95 % Allowed : 2.28 % Favored : 85.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.45 (0.18), residues: 1773 helix: -1.06 (0.16), residues: 822 sheet: -0.81 (0.46), residues: 124 loop : -2.33 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.004 TRP D 327 HIS 0.017 0.002 HIS C 206 PHE 0.021 0.003 PHE D 491 TYR 0.026 0.003 TYR C 311 ARG 0.041 0.003 ARG B 340 Details of bonding type rmsd hydrogen bonds : bond 0.17744 ( 770) hydrogen bonds : angle 8.00788 ( 2169) metal coordination : bond 0.18912 ( 4) metal coordination : angle 27.70161 ( 12) covalent geometry : bond 0.00970 (15941) covalent geometry : angle 1.46804 (21835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 483 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7512 (t70) cc_final: 0.7238 (t70) REVERT: A 143 VAL cc_start: 0.8024 (t) cc_final: 0.6933 (t) REVERT: A 154 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5556 (t70) REVERT: A 256 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7269 (tt0) REVERT: A 358 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: A 420 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6280 (m-40) REVERT: A 557 VAL cc_start: 0.8015 (t) cc_final: 0.7710 (t) REVERT: B 220 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5359 (mmm160) REVERT: B 227 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6216 (mm-40) REVERT: B 248 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5935 (ttp80) REVERT: B 351 LYS cc_start: 0.6667 (tptp) cc_final: 0.6443 (tptt) REVERT: B 479 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6498 (ptt) REVERT: B 488 THR cc_start: 0.8499 (p) cc_final: 0.8250 (p) REVERT: B 518 GLN cc_start: 0.6112 (mp10) cc_final: 0.5423 (mp10) REVERT: C 201 VAL cc_start: 0.7427 (t) cc_final: 0.7147 (p) REVERT: C 227 GLN cc_start: 0.8103 (pp30) cc_final: 0.7622 (pt0) REVERT: C 256 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 336 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6502 (mmm160) REVERT: C 517 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7015 (tm-30) REVERT: C 543 THR cc_start: 0.8724 (p) cc_final: 0.8445 (p) REVERT: D 301 HIS cc_start: 0.7425 (p-80) cc_final: 0.7072 (p90) REVERT: D 379 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1334 (tp) REVERT: D 394 MET cc_start: 0.4757 (mmt) cc_final: 0.4206 (mmt) REVERT: D 457 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7244 (mtm-85) REVERT: D 464 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4045 (tpt) REVERT: D 479 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3279 (tmm) REVERT: D 513 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6613 (pt0) REVERT: D 517 GLU cc_start: 0.5790 (mm-30) cc_final: 0.4496 (tt0) REVERT: E 47 LYS cc_start: 0.8422 (mttm) cc_final: 0.8104 (mttt) REVERT: E 65 ILE cc_start: 0.8467 (pt) cc_final: 0.8214 (pt) REVERT: E 75 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7690 (tptp) REVERT: E 84 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (t) REVERT: F 29 CYS cc_start: 0.7938 (t) cc_final: 0.7620 (m) REVERT: F 32 GLN cc_start: 0.6968 (tp40) cc_final: 0.6688 (tt0) REVERT: F 42 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7314 (tmm160) REVERT: F 91 GLN cc_start: 0.8584 (pm20) cc_final: 0.8365 (pm20) outliers start: 178 outliers final: 27 residues processed: 575 average time/residue: 0.4198 time to fit residues: 320.9727 Evaluate side-chains 288 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 515 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 420 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN B 522 HIS C 310 GLN C 312 GLN C 342 ASN D 274 HIS D 451 HIS ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108025 restraints weight = 28883.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108412 restraints weight = 16566.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109671 restraints weight = 11526.057| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 15945 Z= 0.303 Angle : 1.052 45.739 21847 Z= 0.494 Chirality : 0.053 0.217 2361 Planarity : 0.008 0.168 2644 Dihedral : 18.521 139.143 2797 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 4.90 % Allowed : 15.64 % Favored : 79.46 % 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: -1.53 (0.19), residues: 1773 helix: 0.02 (0.17), residues: 842 sheet: -0.60 (0.45), residues: 130 loop : -2.26 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 327 HIS 0.011 0.002 HIS A 274 PHE 0.026 0.002 PHE B 425 TYR 0.028 0.003 TYR D 527 ARG 0.016 0.001 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.07175 ( 770) hydrogen bonds : angle 5.52139 ( 2169) metal coordination : bond 0.01687 ( 4) metal coordination : angle 21.57589 ( 12) covalent geometry : bond 0.00661 (15941) covalent geometry : angle 0.92280 (21835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 287 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8795 (t0) cc_final: 0.8557 (t0) REVERT: A 69 HIS cc_start: 0.7607 (t70) cc_final: 0.7319 (t-170) REVERT: A 232 TYR cc_start: 0.8372 (t80) cc_final: 0.8137 (t80) REVERT: A 256 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7442 (tt0) REVERT: A 479 MET cc_start: 0.7374 (ttm) cc_final: 0.6956 (ttm) REVERT: A 526 LYS cc_start: 0.8549 (mttm) cc_final: 0.8301 (mptt) REVERT: B 389 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: B 394 MET cc_start: 0.8261 (tpp) cc_final: 0.8017 (mtt) REVERT: B 506 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8576 (mttm) REVERT: C 236 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.7038 (p0) REVERT: C 259 GLN cc_start: 0.8696 (mt0) cc_final: 0.8378 (mt0) REVERT: C 280 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: C 291 TRP cc_start: 0.7479 (t-100) cc_final: 0.6562 (t60) REVERT: C 373 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7318 (pp) REVERT: C 389 GLN cc_start: 0.7780 (mt0) cc_final: 0.7411 (mp10) REVERT: C 418 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.8056 (Cg_endo) REVERT: C 479 MET cc_start: 0.8871 (mmt) cc_final: 0.8502 (mmm) REVERT: C 517 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6921 (tp30) REVERT: D 285 TRP cc_start: 0.7319 (m100) cc_final: 0.7060 (m100) REVERT: D 301 HIS cc_start: 0.7510 (p-80) cc_final: 0.6906 (p90) REVERT: D 379 ILE cc_start: 0.2979 (OUTLIER) cc_final: 0.2580 (tp) REVERT: D 430 LEU cc_start: 0.5776 (mt) cc_final: 0.5358 (mp) REVERT: D 478 LEU cc_start: 0.2727 (pp) cc_final: 0.2481 (pp) REVERT: D 479 MET cc_start: 0.3793 (mtt) cc_final: 0.2839 (tpt) REVERT: E 47 LYS cc_start: 0.9188 (mttm) cc_final: 0.8940 (mttt) REVERT: E 57 ASN cc_start: 0.8088 (t0) cc_final: 0.7703 (t0) REVERT: E 61 ASP cc_start: 0.8518 (m-30) cc_final: 0.8165 (m-30) REVERT: F 83 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8693 (mmtp) REVERT: F 91 GLN cc_start: 0.8526 (pm20) cc_final: 0.8287 (pm20) outliers start: 73 outliers final: 30 residues processed: 337 average time/residue: 0.3225 time to fit residues: 151.4569 Evaluate side-chains 234 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 515 ARG Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 87 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 144 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS C 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100879 restraints weight = 28990.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104596 restraints weight = 14578.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107159 restraints weight = 9735.431| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15945 Z= 0.190 Angle : 0.810 28.659 21847 Z= 0.393 Chirality : 0.046 0.177 2361 Planarity : 0.006 0.139 2644 Dihedral : 17.197 138.880 2703 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.36 % Allowed : 17.45 % Favored : 79.19 % 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: -0.94 (0.19), residues: 1773 helix: 0.67 (0.17), residues: 844 sheet: -0.79 (0.42), residues: 139 loop : -2.09 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 343 HIS 0.009 0.001 HIS B 295 PHE 0.014 0.001 PHE D 508 TYR 0.017 0.002 TYR D 527 ARG 0.008 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.06455 ( 770) hydrogen bonds : angle 5.03011 ( 2169) metal coordination : bond 0.01198 ( 4) metal coordination : angle 12.83965 ( 12) covalent geometry : bond 0.00435 (15941) covalent geometry : angle 0.75249 (21835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7515 (t70) cc_final: 0.7300 (t-170) REVERT: A 146 ARG cc_start: 0.8137 (mmt180) cc_final: 0.7883 (mmt180) REVERT: A 256 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7408 (tt0) REVERT: A 429 MET cc_start: 0.8745 (tmm) cc_final: 0.8145 (tmm) REVERT: A 526 LYS cc_start: 0.8660 (mttm) cc_final: 0.8259 (mptt) REVERT: B 389 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7655 (mm110) REVERT: B 479 MET cc_start: 0.8161 (mmt) cc_final: 0.7794 (mmm) REVERT: B 506 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8549 (mttm) REVERT: C 248 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7635 (mtp-110) REVERT: C 280 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7878 (pp20) REVERT: C 291 TRP cc_start: 0.7209 (t-100) cc_final: 0.6517 (t60) REVERT: C 361 GLN cc_start: 0.9170 (mm110) cc_final: 0.8831 (mm110) REVERT: C 373 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7281 (pp) REVERT: C 465 MET cc_start: 0.8434 (ttt) cc_final: 0.8112 (ttm) REVERT: C 479 MET cc_start: 0.8833 (mmt) cc_final: 0.8486 (mmm) REVERT: C 500 LEU cc_start: 0.7286 (mm) cc_final: 0.6774 (mm) REVERT: C 536 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: D 285 TRP cc_start: 0.7225 (m100) cc_final: 0.6714 (m100) REVERT: D 379 ILE cc_start: 0.3116 (OUTLIER) cc_final: 0.2803 (tp) REVERT: D 430 LEU cc_start: 0.5649 (mt) cc_final: 0.5283 (mp) REVERT: D 478 LEU cc_start: 0.2621 (pp) cc_final: 0.2393 (pp) REVERT: D 516 MET cc_start: 0.4952 (mmm) cc_final: 0.4503 (mmm) REVERT: E 57 ASN cc_start: 0.8107 (t0) cc_final: 0.7794 (t0) REVERT: E 61 ASP cc_start: 0.8566 (m-30) cc_final: 0.8173 (m-30) REVERT: F 75 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7601 (mmmt) REVERT: F 91 GLN cc_start: 0.8459 (pm20) cc_final: 0.8129 (pm20) outliers start: 50 outliers final: 30 residues processed: 252 average time/residue: 0.3301 time to fit residues: 118.1691 Evaluate side-chains 220 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 47 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN E 13 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.151775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109325 restraints weight = 28081.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110383 restraints weight = 14880.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112002 restraints weight = 9915.028| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15945 Z= 0.141 Angle : 0.719 18.065 21847 Z= 0.357 Chirality : 0.044 0.246 2361 Planarity : 0.005 0.129 2644 Dihedral : 16.929 139.735 2695 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.09 % Allowed : 18.19 % Favored : 78.72 % 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: -0.55 (0.19), residues: 1773 helix: 1.06 (0.18), residues: 849 sheet: -0.77 (0.41), residues: 138 loop : -1.97 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 17 HIS 0.005 0.001 HIS A 274 PHE 0.023 0.001 PHE B 407 TYR 0.020 0.001 TYR C 527 ARG 0.016 0.000 ARG D 515 Details of bonding type rmsd hydrogen bonds : bond 0.05787 ( 770) hydrogen bonds : angle 4.72198 ( 2169) metal coordination : bond 0.00652 ( 4) metal coordination : angle 8.99837 ( 12) covalent geometry : bond 0.00316 (15941) covalent geometry : angle 0.68790 (21835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8775 (t0) cc_final: 0.8562 (t0) REVERT: A 105 LYS cc_start: 0.8179 (mttm) cc_final: 0.7775 (mtmm) REVERT: A 120 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 256 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7426 (tt0) REVERT: A 429 MET cc_start: 0.8546 (tmm) cc_final: 0.8125 (tmm) REVERT: A 462 LEU cc_start: 0.8395 (tp) cc_final: 0.7814 (tp) REVERT: A 479 MET cc_start: 0.7347 (ttm) cc_final: 0.7024 (ttm) REVERT: A 485 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7350 (mt-10) REVERT: A 526 LYS cc_start: 0.8676 (mttm) cc_final: 0.8318 (mptt) REVERT: B 389 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7633 (mm-40) REVERT: B 479 MET cc_start: 0.8105 (mmt) cc_final: 0.7795 (mmm) REVERT: C 227 GLN cc_start: 0.8776 (pp30) cc_final: 0.7823 (pt0) REVERT: C 236 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6726 (p0) REVERT: C 291 TRP cc_start: 0.7226 (t-100) cc_final: 0.6662 (t60) REVERT: C 361 GLN cc_start: 0.9081 (mm110) cc_final: 0.8792 (mm110) REVERT: C 373 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7411 (pp) REVERT: C 465 MET cc_start: 0.8308 (ttt) cc_final: 0.8051 (ttt) REVERT: C 500 LEU cc_start: 0.7172 (mm) cc_final: 0.6673 (mm) REVERT: C 517 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7853 (tp30) REVERT: C 536 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 285 TRP cc_start: 0.7487 (m100) cc_final: 0.6938 (m100) REVERT: D 301 HIS cc_start: 0.7502 (p-80) cc_final: 0.7110 (p90) REVERT: D 358 MET cc_start: 0.6209 (mpt) cc_final: 0.5356 (ttp) REVERT: D 379 ILE cc_start: 0.2852 (OUTLIER) cc_final: 0.2577 (tp) REVERT: D 394 MET cc_start: 0.4210 (OUTLIER) cc_final: 0.3726 (mmt) REVERT: D 429 MET cc_start: 0.5632 (mmm) cc_final: 0.4374 (ptp) REVERT: D 430 LEU cc_start: 0.5902 (mt) cc_final: 0.5476 (mp) REVERT: D 451 HIS cc_start: 0.3704 (OUTLIER) cc_final: 0.2652 (m-70) REVERT: D 457 ARG cc_start: 0.6578 (ptt-90) cc_final: 0.6093 (ptt-90) REVERT: E 61 ASP cc_start: 0.8544 (m-30) cc_final: 0.8180 (m-30) REVERT: F 1 MET cc_start: 0.7489 (tpp) cc_final: 0.7173 (tpp) REVERT: F 32 GLN cc_start: 0.8258 (tp40) cc_final: 0.7819 (tt0) REVERT: F 75 LYS cc_start: 0.7636 (mtmm) cc_final: 0.7422 (mmmt) REVERT: F 83 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8455 (mmtp) REVERT: F 91 GLN cc_start: 0.8306 (pm20) cc_final: 0.7869 (pm20) outliers start: 46 outliers final: 24 residues processed: 244 average time/residue: 0.2968 time to fit residues: 104.9710 Evaluate side-chains 217 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 88 optimal weight: 9.9990 chunk 166 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 138 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN C 334 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105451 restraints weight = 29213.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106676 restraints weight = 14806.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108216 restraints weight = 9835.414| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15945 Z= 0.156 Angle : 0.700 14.295 21847 Z= 0.350 Chirality : 0.043 0.209 2361 Planarity : 0.005 0.123 2644 Dihedral : 16.654 139.685 2690 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.69 % Allowed : 19.13 % Favored : 77.18 % 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: -0.43 (0.20), residues: 1773 helix: 1.17 (0.18), residues: 850 sheet: -0.76 (0.42), residues: 149 loop : -1.91 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 327 HIS 0.005 0.001 HIS A 274 PHE 0.016 0.001 PHE D 391 TYR 0.015 0.001 TYR D 527 ARG 0.007 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.05748 ( 770) hydrogen bonds : angle 4.59540 ( 2169) metal coordination : bond 0.00589 ( 4) metal coordination : angle 7.67587 ( 12) covalent geometry : bond 0.00357 (15941) covalent geometry : angle 0.67681 (21835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8808 (t0) cc_final: 0.8522 (t0) REVERT: A 105 LYS cc_start: 0.8155 (mttm) cc_final: 0.7760 (mtmm) REVERT: A 120 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 256 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7469 (tt0) REVERT: A 429 MET cc_start: 0.8640 (tmm) cc_final: 0.8348 (tmm) REVERT: A 462 LEU cc_start: 0.8535 (tp) cc_final: 0.7929 (tp) REVERT: A 479 MET cc_start: 0.7399 (ttm) cc_final: 0.7125 (ttm) REVERT: A 485 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7559 (mt-10) REVERT: A 526 LYS cc_start: 0.8704 (mttm) cc_final: 0.8304 (mptt) REVERT: B 366 HIS cc_start: 0.7781 (m-70) cc_final: 0.7447 (m-70) REVERT: B 389 GLN cc_start: 0.7897 (mp10) cc_final: 0.7695 (mm-40) REVERT: C 227 GLN cc_start: 0.8665 (pp30) cc_final: 0.7926 (pt0) REVERT: C 236 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6848 (p0) REVERT: C 291 TRP cc_start: 0.7268 (t-100) cc_final: 0.6639 (t60) REVERT: C 517 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8030 (tp30) REVERT: C 518 GLN cc_start: 0.6796 (tp-100) cc_final: 0.6592 (tp40) REVERT: C 536 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 301 HIS cc_start: 0.7683 (p-80) cc_final: 0.7298 (p90) REVERT: D 358 MET cc_start: 0.6269 (mpt) cc_final: 0.5454 (ttp) REVERT: D 368 MET cc_start: 0.5114 (mtt) cc_final: 0.4757 (mtm) REVERT: D 394 MET cc_start: 0.4094 (OUTLIER) cc_final: 0.3587 (mmt) REVERT: D 413 ARG cc_start: 0.2206 (OUTLIER) cc_final: 0.0177 (mtm110) REVERT: D 430 LEU cc_start: 0.6107 (mt) cc_final: 0.5592 (mp) REVERT: D 451 HIS cc_start: 0.3674 (OUTLIER) cc_final: 0.2693 (m-70) REVERT: D 464 MET cc_start: 0.5250 (tpp) cc_final: 0.4990 (tpp) REVERT: E 53 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8714 (m-40) REVERT: E 61 ASP cc_start: 0.8579 (m-30) cc_final: 0.8213 (m-30) REVERT: F 32 GLN cc_start: 0.8250 (tp40) cc_final: 0.7860 (tt0) REVERT: F 91 GLN cc_start: 0.8409 (pm20) cc_final: 0.7928 (pm20) outliers start: 55 outliers final: 30 residues processed: 251 average time/residue: 0.3200 time to fit residues: 117.7466 Evaluate side-chains 223 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 22 optimal weight: 0.0030 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 361 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104350 restraints weight = 28241.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107879 restraints weight = 14043.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110353 restraints weight = 9286.713| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15945 Z= 0.132 Angle : 0.677 14.547 21847 Z= 0.339 Chirality : 0.042 0.180 2361 Planarity : 0.005 0.116 2644 Dihedral : 16.559 139.619 2686 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.68 % Allowed : 21.07 % Favored : 76.24 % 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: -0.28 (0.20), residues: 1773 helix: 1.30 (0.18), residues: 842 sheet: -0.70 (0.42), residues: 149 loop : -1.80 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 327 HIS 0.005 0.001 HIS C 366 PHE 0.021 0.001 PHE B 407 TYR 0.016 0.001 TYR C 527 ARG 0.006 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 770) hydrogen bonds : angle 4.50578 ( 2169) metal coordination : bond 0.00406 ( 4) metal coordination : angle 6.51794 ( 12) covalent geometry : bond 0.00292 (15941) covalent geometry : angle 0.65960 (21835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8752 (t0) cc_final: 0.8522 (t0) REVERT: A 105 LYS cc_start: 0.8127 (mttm) cc_final: 0.7738 (mtmm) REVERT: A 120 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: A 166 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: A 256 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7382 (tt0) REVERT: A 429 MET cc_start: 0.8609 (tmm) cc_final: 0.8357 (tmm) REVERT: A 462 LEU cc_start: 0.8470 (tp) cc_final: 0.7810 (tp) REVERT: A 479 MET cc_start: 0.7488 (ttm) cc_final: 0.7092 (ttm) REVERT: A 485 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7579 (mt-10) REVERT: A 516 MET cc_start: 0.8838 (mmm) cc_final: 0.7949 (mtp) REVERT: A 536 GLU cc_start: 0.7905 (tt0) cc_final: 0.7301 (mt-10) REVERT: B 366 HIS cc_start: 0.7641 (m-70) cc_final: 0.7354 (m-70) REVERT: B 416 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7884 (mmtt) REVERT: C 227 GLN cc_start: 0.8677 (pp30) cc_final: 0.7970 (pt0) REVERT: C 291 TRP cc_start: 0.7124 (t-100) cc_final: 0.6532 (t60) REVERT: C 465 MET cc_start: 0.8416 (ttt) cc_final: 0.8144 (ttm) REVERT: C 500 LEU cc_start: 0.7154 (mm) cc_final: 0.6522 (mm) REVERT: C 517 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8077 (tp30) REVERT: C 518 GLN cc_start: 0.6863 (tp-100) cc_final: 0.6647 (tp40) REVERT: C 536 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: D 230 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4243 (tptp) REVERT: D 285 TRP cc_start: 0.7454 (m100) cc_final: 0.7231 (m100) REVERT: D 301 HIS cc_start: 0.7699 (p-80) cc_final: 0.6631 (p90) REVERT: D 358 MET cc_start: 0.5580 (mpt) cc_final: 0.4984 (ttt) REVERT: D 413 ARG cc_start: 0.1557 (OUTLIER) cc_final: 0.0484 (mtm110) REVERT: D 429 MET cc_start: 0.5460 (mmm) cc_final: 0.4248 (ptp) REVERT: D 431 THR cc_start: 0.6003 (p) cc_final: 0.5415 (p) REVERT: D 451 HIS cc_start: 0.3398 (OUTLIER) cc_final: 0.2514 (m-70) REVERT: D 479 MET cc_start: 0.1857 (mmt) cc_final: 0.1558 (mmt) REVERT: E 22 LYS cc_start: 0.8855 (pttt) cc_final: 0.8559 (ptpt) REVERT: E 61 ASP cc_start: 0.8439 (m-30) cc_final: 0.8077 (m-30) REVERT: F 32 GLN cc_start: 0.8157 (tp40) cc_final: 0.7875 (tt0) REVERT: F 91 GLN cc_start: 0.8381 (pm20) cc_final: 0.7813 (pm20) outliers start: 40 outliers final: 19 residues processed: 237 average time/residue: 0.2956 time to fit residues: 101.0050 Evaluate side-chains 221 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 0.1980 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 140 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 538 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.150675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102088 restraints weight = 28815.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105622 restraints weight = 14681.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108051 restraints weight = 9858.058| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15945 Z= 0.135 Angle : 0.663 14.098 21847 Z= 0.333 Chirality : 0.042 0.145 2361 Planarity : 0.005 0.112 2644 Dihedral : 16.511 139.776 2686 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.89 % Allowed : 21.14 % Favored : 75.97 % 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: -0.19 (0.20), residues: 1773 helix: 1.36 (0.18), residues: 850 sheet: -0.83 (0.40), residues: 165 loop : -1.75 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 327 HIS 0.005 0.001 HIS C 366 PHE 0.016 0.001 PHE D 391 TYR 0.023 0.001 TYR C 387 ARG 0.007 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.05454 ( 770) hydrogen bonds : angle 4.41183 ( 2169) metal coordination : bond 0.00425 ( 4) metal coordination : angle 6.25367 ( 12) covalent geometry : bond 0.00308 (15941) covalent geometry : angle 0.64659 (21835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8724 (t0) cc_final: 0.8509 (t0) REVERT: A 105 LYS cc_start: 0.8132 (mttm) cc_final: 0.7765 (mtmm) REVERT: A 120 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 256 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7184 (tt0) REVERT: A 351 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7435 (mmtt) REVERT: A 358 MET cc_start: 0.7527 (mmp) cc_final: 0.6084 (tmm) REVERT: A 462 LEU cc_start: 0.8556 (tp) cc_final: 0.8239 (mp) REVERT: A 479 MET cc_start: 0.7541 (ttm) cc_final: 0.7167 (ttm) REVERT: A 516 MET cc_start: 0.8868 (mmm) cc_final: 0.7981 (mtp) REVERT: A 536 GLU cc_start: 0.7790 (tt0) cc_final: 0.7238 (mt-10) REVERT: B 366 HIS cc_start: 0.7887 (m-70) cc_final: 0.7676 (m-70) REVERT: C 227 GLN cc_start: 0.8682 (pp30) cc_final: 0.8025 (pt0) REVERT: C 247 VAL cc_start: 0.8685 (t) cc_final: 0.8351 (p) REVERT: C 291 TRP cc_start: 0.7194 (t-100) cc_final: 0.6653 (t60) REVERT: C 465 MET cc_start: 0.8378 (ttt) cc_final: 0.8083 (ttm) REVERT: C 500 LEU cc_start: 0.7110 (mm) cc_final: 0.6506 (mm) REVERT: C 517 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8086 (tp30) REVERT: C 536 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: D 230 LYS cc_start: 0.5248 (OUTLIER) cc_final: 0.4078 (tppt) REVERT: D 253 ARG cc_start: 0.7370 (tpt90) cc_final: 0.6437 (ptp-110) REVERT: D 259 GLN cc_start: 0.5159 (pm20) cc_final: 0.4946 (pm20) REVERT: D 285 TRP cc_start: 0.7430 (m100) cc_final: 0.7173 (m100) REVERT: D 301 HIS cc_start: 0.7702 (p-80) cc_final: 0.7452 (p90) REVERT: D 325 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7675 (mpt180) REVERT: D 358 MET cc_start: 0.5839 (mpt) cc_final: 0.5305 (ttt) REVERT: D 413 ARG cc_start: 0.1392 (OUTLIER) cc_final: 0.0444 (mtm110) REVERT: D 429 MET cc_start: 0.5581 (mmm) cc_final: 0.4347 (ptp) REVERT: D 444 ASP cc_start: 0.6881 (t0) cc_final: 0.6551 (t0) REVERT: D 451 HIS cc_start: 0.3478 (OUTLIER) cc_final: 0.2687 (m-70) REVERT: D 468 PHE cc_start: 0.7349 (m-80) cc_final: 0.7102 (m-80) REVERT: E 22 LYS cc_start: 0.8901 (pttt) cc_final: 0.8657 (ptpt) REVERT: E 60 GLU cc_start: 0.6967 (pm20) cc_final: 0.6643 (pm20) REVERT: E 61 ASP cc_start: 0.8445 (m-30) cc_final: 0.8050 (m-30) REVERT: F 24 MET cc_start: 0.8770 (tpp) cc_final: 0.8562 (tpt) REVERT: F 91 GLN cc_start: 0.8428 (pm20) cc_final: 0.7873 (pm20) outliers start: 43 outliers final: 23 residues processed: 243 average time/residue: 0.2921 time to fit residues: 102.4241 Evaluate side-chains 221 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103611 restraints weight = 27779.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107210 restraints weight = 13841.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109524 restraints weight = 9073.608| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15945 Z= 0.136 Angle : 0.668 13.643 21847 Z= 0.337 Chirality : 0.042 0.169 2361 Planarity : 0.005 0.109 2644 Dihedral : 16.452 139.275 2686 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.15 % Allowed : 21.41 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1773 helix: 1.39 (0.18), residues: 848 sheet: -0.80 (0.40), residues: 165 loop : -1.75 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 327 HIS 0.007 0.001 HIS C 366 PHE 0.013 0.001 PHE D 391 TYR 0.018 0.001 TYR C 387 ARG 0.009 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05452 ( 770) hydrogen bonds : angle 4.40499 ( 2169) metal coordination : bond 0.00446 ( 4) metal coordination : angle 5.97728 ( 12) covalent geometry : bond 0.00307 (15941) covalent geometry : angle 0.65299 (21835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8730 (t0) cc_final: 0.8513 (t0) REVERT: A 105 LYS cc_start: 0.8085 (mttm) cc_final: 0.7767 (mtmm) REVERT: A 120 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: A 145 SER cc_start: 0.8760 (m) cc_final: 0.8280 (p) REVERT: A 256 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7196 (tt0) REVERT: A 358 MET cc_start: 0.7310 (mmp) cc_final: 0.6087 (tmm) REVERT: A 374 GLU cc_start: 0.8168 (mp0) cc_final: 0.7909 (pm20) REVERT: A 429 MET cc_start: 0.8694 (tmm) cc_final: 0.8277 (tmm) REVERT: A 462 LEU cc_start: 0.8600 (tp) cc_final: 0.8300 (mp) REVERT: A 479 MET cc_start: 0.7556 (ttm) cc_final: 0.7192 (ttm) REVERT: A 516 MET cc_start: 0.8863 (mmm) cc_final: 0.7999 (mtp) REVERT: A 536 GLU cc_start: 0.7728 (tt0) cc_final: 0.7292 (mt-10) REVERT: C 227 GLN cc_start: 0.8625 (pp30) cc_final: 0.7988 (pt0) REVERT: C 247 VAL cc_start: 0.8557 (t) cc_final: 0.8233 (p) REVERT: C 291 TRP cc_start: 0.7237 (t-100) cc_final: 0.6684 (t60) REVERT: C 465 MET cc_start: 0.8381 (ttt) cc_final: 0.8058 (ttm) REVERT: C 500 LEU cc_start: 0.7029 (mm) cc_final: 0.6412 (mm) REVERT: C 517 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8074 (tp30) REVERT: C 536 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: D 230 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4131 (tptt) REVERT: D 253 ARG cc_start: 0.7352 (tpt90) cc_final: 0.6399 (ptp-110) REVERT: D 301 HIS cc_start: 0.7738 (p-80) cc_final: 0.7526 (p90) REVERT: D 325 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7716 (mpt180) REVERT: D 358 MET cc_start: 0.5833 (mpt) cc_final: 0.5290 (ttt) REVERT: D 413 ARG cc_start: 0.1529 (OUTLIER) cc_final: 0.0466 (mtm110) REVERT: D 429 MET cc_start: 0.5771 (mmm) cc_final: 0.4822 (ptp) REVERT: D 444 ASP cc_start: 0.6869 (t0) cc_final: 0.6551 (t0) REVERT: D 451 HIS cc_start: 0.3373 (OUTLIER) cc_final: 0.2641 (m-70) REVERT: E 22 LYS cc_start: 0.8897 (pttt) cc_final: 0.8664 (ptpt) REVERT: E 25 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.7974 (m-70) REVERT: E 61 ASP cc_start: 0.8446 (m-30) cc_final: 0.8109 (m-30) REVERT: F 91 GLN cc_start: 0.8492 (pm20) cc_final: 0.7904 (pm20) outliers start: 47 outliers final: 25 residues processed: 244 average time/residue: 0.2911 time to fit residues: 103.0630 Evaluate side-chains 230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 62.966 > 50: distance: 32 - 48: 21.631 distance: 44 - 48: 21.621 distance: 48 - 49: 46.638 distance: 49 - 50: 40.032 distance: 50 - 51: 34.003 distance: 50 - 52: 25.082 distance: 52 - 53: 38.714 distance: 53 - 54: 10.812 distance: 53 - 56: 30.102 distance: 54 - 55: 19.648 distance: 54 - 59: 40.574 distance: 56 - 57: 27.594 distance: 56 - 58: 21.666 distance: 59 - 60: 21.865 distance: 60 - 61: 14.776 distance: 60 - 63: 18.453 distance: 61 - 62: 49.537 distance: 61 - 67: 55.757 distance: 63 - 64: 45.550 distance: 64 - 65: 33.770 distance: 65 - 66: 29.134 distance: 67 - 68: 58.110 distance: 67 - 73: 30.303 distance: 68 - 69: 52.698 distance: 68 - 71: 30.343 distance: 69 - 70: 44.703 distance: 69 - 74: 50.378 distance: 71 - 72: 28.684 distance: 72 - 73: 36.388 distance: 74 - 75: 13.927 distance: 74 - 80: 36.187 distance: 75 - 76: 13.167 distance: 75 - 78: 26.161 distance: 76 - 77: 34.123 distance: 76 - 81: 34.368 distance: 78 - 79: 26.301 distance: 79 - 80: 35.143 distance: 81 - 82: 24.822 distance: 81 - 87: 44.097 distance: 82 - 83: 17.822 distance: 82 - 85: 29.437 distance: 83 - 84: 21.240 distance: 83 - 88: 8.673 distance: 85 - 86: 41.341 distance: 86 - 87: 26.380 distance: 88 - 89: 11.872 distance: 89 - 90: 49.180 distance: 89 - 92: 42.267 distance: 90 - 91: 48.016 distance: 90 - 96: 54.010 distance: 92 - 93: 52.519 distance: 93 - 94: 56.924 distance: 93 - 95: 47.372 distance: 96 - 97: 10.822 distance: 97 - 98: 22.322 distance: 97 - 100: 40.382 distance: 98 - 99: 34.867 distance: 98 - 105: 11.360 distance: 100 - 101: 10.287 distance: 101 - 102: 23.174 distance: 102 - 103: 28.547 distance: 102 - 104: 32.766 distance: 105 - 106: 29.572 distance: 106 - 107: 40.082 distance: 106 - 109: 33.939 distance: 107 - 108: 30.714 distance: 107 - 113: 20.634 distance: 109 - 110: 35.860 distance: 110 - 111: 16.161 distance: 110 - 112: 12.771 distance: 113 - 114: 15.947 distance: 114 - 115: 45.134 distance: 114 - 117: 14.806 distance: 115 - 116: 25.455 distance: 115 - 119: 26.795 distance: 117 - 118: 44.303