Starting phenix.real_space_refine on Sat Jul 4 11:57:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iaj_35304/07_2026/8iaj_35304.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 13350 2.51 5 N 3470 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "F" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "H" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.23 Number of scatterers: 20768 At special positions: 0 Unit cell: (171.72, 106.92, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3832 8.00 N 3470 7.00 C 13350 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 51.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.744A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 482 through 504 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.898A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.823A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.614A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 532 " --> pdb=" O GLY B 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 528 through 532' Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE D 145 " --> pdb=" O MET D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 170 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 53 through 75 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 279 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 389 through 405 removed outlier: 3.743A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 Processing helix chain 'E' and resid 482 through 504 Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.899A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE F 122 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.824A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.615A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR F 423 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 532 " --> pdb=" O GLY F 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 528 through 532' Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE H 88 " --> pdb=" O HIS H 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE H 145 " --> pdb=" O MET H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 170 Proline residue: H 162 - end of helix Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 Processing helix chain 'G' and resid 53 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 148 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY A 207 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B 153 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 140 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 151 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS B 142 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 149 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP B 218 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 363 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 246 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AA8, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY E 207 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 138 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA F 153 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE F 140 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER F 151 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS F 142 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR F 149 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP F 218 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR F 363 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F 246 " --> pdb=" O CYS F 300 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 52 985 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6624 1.34 - 1.47: 5000 1.47 - 1.59: 9432 1.59 - 1.71: 2 1.71 - 1.83: 174 Bond restraints: 21232 Sorted by residual: bond pdb=" C14 Z1T F 602 " pdb=" C15 Z1T F 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C14 Z1T B 602 " pdb=" C15 Z1T B 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C3 PLP F 601 " pdb=" C4 PLP F 601 " ideal model delta sigma weight residual 1.402 1.480 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.402 1.480 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.687 1.610 0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 21227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 28678 4.54 - 9.07: 88 9.07 - 13.61: 2 13.61 - 18.15: 0 18.15 - 22.68: 4 Bond angle restraints: 28772 Sorted by residual: angle pdb=" CB MET D 70 " pdb=" CG MET D 70 " pdb=" SD MET D 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 70 " pdb=" CG MET H 70 " pdb=" SD MET H 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 177 " pdb=" CG MET H 177 " pdb=" SD MET H 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" CB MET D 177 " pdb=" CG MET D 177 " pdb=" SD MET D 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N MET B 307 " pdb=" CA MET B 307 " pdb=" C MET B 307 " ideal model delta sigma weight residual 114.64 107.24 7.40 1.52e+00 4.33e-01 2.37e+01 ... (remaining 28767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 11798 21.06 - 42.12: 866 42.12 - 63.18: 90 63.18 - 84.24: 16 84.24 - 105.30: 6 Dihedral angle restraints: 12776 sinusoidal: 5186 harmonic: 7590 Sorted by residual: dihedral pdb=" CA GLY D 134 " pdb=" C GLY D 134 " pdb=" N ALA D 135 " pdb=" CA ALA D 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLY H 134 " pdb=" C GLY H 134 " pdb=" N ALA H 135 " pdb=" CA ALA H 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PHE A 256 " pdb=" C PHE A 256 " pdb=" N ASN A 257 " pdb=" CA ASN A 257 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2338 0.048 - 0.095: 749 0.095 - 0.143: 153 0.143 - 0.190: 12 0.190 - 0.238: 4 Chirality restraints: 3256 Sorted by residual: chirality pdb=" CA LEU B 91 " pdb=" N LEU B 91 " pdb=" C LEU B 91 " pdb=" CB LEU B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU F 91 " pdb=" N LEU F 91 " pdb=" C LEU F 91 " pdb=" CB LEU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C17 Z1T F 602 " pdb=" C16 Z1T F 602 " pdb=" C18 Z1T F 602 " pdb=" N1 Z1T F 602 " both_signs ideal model delta sigma weight residual False 2.47 2.69 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3253 not shown) Planarity restraints: 3652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 86 " 0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A 87 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 86 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO E 87 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 48 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C PHE G 48 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE G 48 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR G 49 " -0.014 2.00e-02 2.50e+03 ... (remaining 3649 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1062 2.72 - 3.27: 20149 3.27 - 3.81: 32021 3.81 - 4.36: 38933 4.36 - 4.90: 70221 Nonbonded interactions: 162386 Sorted by model distance: nonbonded pdb=" CD LYS A 85 " pdb=" OE1 GLN H 55 " model vdw 2.176 3.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD2 ASP D 63 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG E 228 " pdb=" OD2 ASP H 63 " model vdw 2.184 3.120 nonbonded pdb=" OE1 GLN D 55 " pdb=" CD LYS E 85 " model vdw 2.193 3.440 nonbonded pdb=" OG1 THR F 342 " pdb=" OE2 GLU F 348 " model vdw 2.204 3.040 ... (remaining 162381 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.920 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 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 : 0.008 0.463 21234 Z= 0.527 Angle : 0.852 22.682 28772 Z= 0.483 Chirality : 0.047 0.238 3256 Planarity : 0.005 0.069 3652 Dihedral : 13.932 105.296 7888 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 0.61 % Allowed : 0.78 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2582 helix: 1.50 (0.15), residues: 1218 sheet: -0.46 (0.32), residues: 258 loop : -2.21 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 42 TYR 0.022 0.002 TYR F 533 PHE 0.036 0.002 PHE C 62 TRP 0.010 0.001 TRP D 106 HIS 0.004 0.001 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.28 (21232) covalent geometry : angle 0.85181 / 0.48 (28772) hydrogen bonds : bond 0.15985 / 10.58 ( 985) hydrogen bonds : angle 5.88274 / 4.21 ( 2889) Misc. bond : bond 0.46243 / 27.35 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 THR cc_start: 0.8399 (p) cc_final: 0.8098 (p) REVERT: F 466 MET cc_start: 0.8273 (ttp) cc_final: 0.7822 (ttp) REVERT: H 39 THR cc_start: 0.8395 (p) cc_final: 0.8078 (p) outliers start: 14 outliers final: 5 residues processed: 270 average time/residue: 0.1491 time to fit residues: 62.8064 Evaluate side-chains 212 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 237 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 145 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 237 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 145 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097919 restraints weight = 28460.916| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.67 r_work: 0.2916 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21234 Z= 0.143 Angle : 0.594 6.909 28772 Z= 0.317 Chirality : 0.044 0.181 3256 Planarity : 0.005 0.046 3652 Dihedral : 7.763 100.044 2939 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.00 % Allowed : 6.30 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2582 helix: 1.77 (0.15), residues: 1230 sheet: 0.07 (0.31), residues: 280 loop : -2.12 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 174 TYR 0.015 0.001 TYR F 510 PHE 0.017 0.001 PHE E 256 TRP 0.009 0.001 TRP H 142 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (21232) covalent geometry : angle 0.59376 / 0.32 (28772) hydrogen bonds : bond 0.05302 / 3.52 ( 985) hydrogen bonds : angle 4.64339 / 3.30 ( 2889) Misc. bond : bond 0.00139 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.818 Fit side-chains REVERT: A 94 ASP cc_start: 0.8330 (m-30) cc_final: 0.7891 (m-30) REVERT: A 261 MET cc_start: 0.8253 (mmp) cc_final: 0.7907 (mmp) REVERT: B 396 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: D 39 THR cc_start: 0.8392 (p) cc_final: 0.8065 (p) REVERT: D 73 THR cc_start: 0.9176 (m) cc_final: 0.8849 (p) REVERT: C 59 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8527 (tp) REVERT: E 94 ASP cc_start: 0.8309 (m-30) cc_final: 0.7853 (m-30) REVERT: E 261 MET cc_start: 0.8308 (mmp) cc_final: 0.7931 (mmp) REVERT: F 396 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: F 520 ASP cc_start: 0.8113 (t0) cc_final: 0.7902 (m-30) REVERT: H 39 THR cc_start: 0.8404 (p) cc_final: 0.8081 (p) REVERT: H 73 THR cc_start: 0.9176 (m) cc_final: 0.8853 (p) REVERT: G 59 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8529 (tp) outliers start: 23 outliers final: 13 residues processed: 266 average time/residue: 0.1416 time to fit residues: 59.1164 Evaluate side-chains 228 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 26 optimal weight: 0.0270 chunk 182 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 160 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 overall best weight: 2.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096193 restraints weight = 28264.569| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.78 r_work: 0.2904 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21234 Z= 0.157 Angle : 0.588 6.863 28772 Z= 0.312 Chirality : 0.044 0.178 3256 Planarity : 0.005 0.053 3652 Dihedral : 7.256 96.137 2933 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.30 % Allowed : 8.61 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2582 helix: 1.86 (0.15), residues: 1218 sheet: 0.40 (0.33), residues: 256 loop : -2.00 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 174 TYR 0.017 0.001 TYR B 510 PHE 0.019 0.001 PHE E 256 TRP 0.009 0.001 TRP D 142 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (21232) covalent geometry : angle 0.58760 / 0.31 (28772) hydrogen bonds : bond 0.05358 / 3.55 ( 985) hydrogen bonds : angle 4.46246 / 3.18 ( 2889) Misc. bond : bond 0.00111 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.566 Fit side-chains REVERT: A 85 LYS cc_start: 0.8587 (tppt) cc_final: 0.8360 (mmtp) REVERT: A 98 ASP cc_start: 0.8182 (m-30) cc_final: 0.7906 (m-30) REVERT: B 396 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: D 39 THR cc_start: 0.8281 (p) cc_final: 0.7943 (p) REVERT: C 59 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8513 (tp) REVERT: E 85 LYS cc_start: 0.8585 (tppt) cc_final: 0.8169 (tppt) REVERT: E 98 ASP cc_start: 0.8192 (m-30) cc_final: 0.7920 (m-30) REVERT: F 396 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: H 39 THR cc_start: 0.8301 (p) cc_final: 0.7954 (p) REVERT: G 59 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8504 (tp) outliers start: 30 outliers final: 25 residues processed: 246 average time/residue: 0.1430 time to fit residues: 55.5268 Evaluate side-chains 246 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 110 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100223 restraints weight = 28184.282| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.78 r_work: 0.2957 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 21234 Z= 0.107 Angle : 0.515 6.451 28772 Z= 0.274 Chirality : 0.041 0.184 3256 Planarity : 0.005 0.051 3652 Dihedral : 6.989 93.861 2933 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.35 % Allowed : 9.91 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2582 helix: 1.99 (0.15), residues: 1232 sheet: 0.57 (0.33), residues: 256 loop : -1.79 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 496 TYR 0.013 0.001 TYR B 510 PHE 0.015 0.001 PHE G 62 TRP 0.007 0.001 TRP F 294 HIS 0.002 0.001 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21232) covalent geometry : angle 0.51514 / 0.27 (28772) hydrogen bonds : bond 0.03984 / 2.66 ( 985) hydrogen bonds : angle 4.27309 / 3.05 ( 2889) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.825 Fit side-chains REVERT: A 94 ASP cc_start: 0.7995 (m-30) cc_final: 0.7692 (m-30) REVERT: A 98 ASP cc_start: 0.8149 (m-30) cc_final: 0.7758 (m-30) REVERT: A 308 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8267 (ttmm) REVERT: B 483 VAL cc_start: 0.8697 (m) cc_final: 0.8440 (t) REVERT: B 520 ASP cc_start: 0.8177 (t0) cc_final: 0.7685 (m-30) REVERT: D 39 THR cc_start: 0.8234 (p) cc_final: 0.7905 (p) REVERT: D 42 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7120 (mtm180) REVERT: C 59 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8539 (tp) REVERT: E 94 ASP cc_start: 0.7991 (m-30) cc_final: 0.7705 (m-30) REVERT: E 98 ASP cc_start: 0.8161 (m-30) cc_final: 0.7780 (m-30) REVERT: E 308 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8258 (ttmm) REVERT: F 466 MET cc_start: 0.8568 (ttp) cc_final: 0.8315 (ttp) REVERT: F 483 VAL cc_start: 0.8696 (m) cc_final: 0.8410 (t) REVERT: F 520 ASP cc_start: 0.8159 (t0) cc_final: 0.7668 (m-30) REVERT: H 39 THR cc_start: 0.8244 (p) cc_final: 0.7903 (p) REVERT: H 42 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7117 (mtm180) REVERT: G 59 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (tp) outliers start: 31 outliers final: 19 residues processed: 253 average time/residue: 0.1496 time to fit residues: 59.6889 Evaluate side-chains 238 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 57 optimal weight: 0.5980 chunk 224 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 58 optimal weight: 0.0020 chunk 236 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 130 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095701 restraints weight = 28062.547| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.77 r_work: 0.2896 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21234 Z= 0.167 Angle : 0.586 8.023 28772 Z= 0.310 Chirality : 0.044 0.172 3256 Planarity : 0.005 0.057 3652 Dihedral : 7.063 94.638 2933 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.22 % Allowed : 10.83 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2582 helix: 1.92 (0.15), residues: 1226 sheet: 0.45 (0.33), residues: 254 loop : -1.80 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 174 TYR 0.024 0.002 TYR E 460 PHE 0.021 0.002 PHE F 236 TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (21232) covalent geometry : angle 0.58603 / 0.31 (28772) hydrogen bonds : bond 0.05315 / 3.52 ( 985) hydrogen bonds : angle 4.33192 / 3.09 ( 2889) Misc. bond : bond 0.00096 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.814 Fit side-chains REVERT: A 85 LYS cc_start: 0.8593 (tppt) cc_final: 0.8235 (tppt) REVERT: A 261 MET cc_start: 0.8227 (mmp) cc_final: 0.7833 (mmp) REVERT: B 139 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7675 (mtm180) REVERT: B 396 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: B 466 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8445 (mtp) REVERT: D 39 THR cc_start: 0.8280 (p) cc_final: 0.7944 (p) REVERT: C 59 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (tp) REVERT: E 85 LYS cc_start: 0.8534 (tppt) cc_final: 0.8170 (tppt) REVERT: F 139 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7696 (mtm180) REVERT: F 396 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: H 39 THR cc_start: 0.8292 (p) cc_final: 0.7952 (p) REVERT: G 59 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8570 (tp) outliers start: 51 outliers final: 37 residues processed: 252 average time/residue: 0.1388 time to fit residues: 55.4562 Evaluate side-chains 255 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 208 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096608 restraints weight = 28146.247| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.77 r_work: 0.2897 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21234 Z= 0.148 Angle : 0.568 10.010 28772 Z= 0.299 Chirality : 0.043 0.174 3256 Planarity : 0.005 0.058 3652 Dihedral : 6.990 93.991 2933 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 12.39 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2582 helix: 1.92 (0.15), residues: 1234 sheet: 0.47 (0.33), residues: 254 loop : -1.77 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 174 TYR 0.017 0.001 TYR B 510 PHE 0.019 0.001 PHE C 62 TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21232) covalent geometry : angle 0.56801 / 0.30 (28772) hydrogen bonds : bond 0.04964 / 3.30 ( 985) hydrogen bonds : angle 4.30384 / 3.08 ( 2889) Misc. bond : bond 0.00092 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.743 Fit side-chains REVERT: A 261 MET cc_start: 0.8234 (mmp) cc_final: 0.7795 (mmp) REVERT: B 139 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: B 396 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: D 39 THR cc_start: 0.8263 (p) cc_final: 0.7931 (p) REVERT: C 14 THR cc_start: 0.7836 (p) cc_final: 0.7564 (p) REVERT: C 59 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8536 (tp) REVERT: F 116 MET cc_start: 0.8621 (mmm) cc_final: 0.8318 (mmp) REVERT: F 139 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7897 (mtm180) REVERT: F 396 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: H 39 THR cc_start: 0.8270 (p) cc_final: 0.7935 (p) REVERT: G 14 THR cc_start: 0.7860 (p) cc_final: 0.7587 (p) REVERT: G 59 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (tp) outliers start: 45 outliers final: 30 residues processed: 255 average time/residue: 0.1391 time to fit residues: 55.7322 Evaluate side-chains 249 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096054 restraints weight = 28322.070| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.79 r_work: 0.2893 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21234 Z= 0.148 Angle : 0.568 9.356 28772 Z= 0.299 Chirality : 0.043 0.174 3256 Planarity : 0.005 0.057 3652 Dihedral : 6.962 93.952 2932 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.30 % Allowed : 12.70 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2582 helix: 1.93 (0.15), residues: 1234 sheet: 0.55 (0.33), residues: 254 loop : -1.76 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 174 TYR 0.017 0.001 TYR B 510 PHE 0.019 0.001 PHE C 62 TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21232) covalent geometry : angle 0.56846 / 0.30 (28772) hydrogen bonds : bond 0.04975 / 3.31 ( 985) hydrogen bonds : angle 4.28694 / 3.06 ( 2889) Misc. bond : bond 0.00084 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.559 Fit side-chains REVERT: A 261 MET cc_start: 0.8247 (mmp) cc_final: 0.7819 (mmp) REVERT: A 308 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8260 (ttmm) REVERT: B 139 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7901 (mtm180) REVERT: B 396 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: D 39 THR cc_start: 0.8272 (p) cc_final: 0.7919 (p) REVERT: C 14 THR cc_start: 0.7887 (p) cc_final: 0.7601 (p) REVERT: C 59 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8553 (tp) REVERT: F 116 MET cc_start: 0.8607 (mmm) cc_final: 0.8310 (mmp) REVERT: F 139 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7915 (mtm180) REVERT: F 396 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7692 (pp20) REVERT: H 39 THR cc_start: 0.8271 (p) cc_final: 0.7917 (p) REVERT: G 14 THR cc_start: 0.7892 (p) cc_final: 0.7608 (p) REVERT: G 59 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (tp) outliers start: 53 outliers final: 36 residues processed: 260 average time/residue: 0.1333 time to fit residues: 54.9212 Evaluate side-chains 256 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 464 GLN H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099725 restraints weight = 28075.110| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.78 r_work: 0.2947 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21234 Z= 0.106 Angle : 0.514 8.863 28772 Z= 0.271 Chirality : 0.041 0.179 3256 Planarity : 0.005 0.053 3652 Dihedral : 6.773 92.936 2932 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.04 % Allowed : 12.91 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2582 helix: 2.10 (0.15), residues: 1234 sheet: 0.68 (0.33), residues: 256 loop : -1.62 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.013 0.001 TYR F 510 PHE 0.018 0.001 PHE C 62 TRP 0.008 0.001 TRP F 294 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21232) covalent geometry : angle 0.51397 / 0.27 (28772) hydrogen bonds : bond 0.03920 / 2.62 ( 985) hydrogen bonds : angle 4.19133 / 3.00 ( 2889) Misc. bond : bond 0.00044 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.781 Fit side-chains REVERT: A 85 LYS cc_start: 0.8558 (tppt) cc_final: 0.8265 (tppt) REVERT: A 261 MET cc_start: 0.8192 (mmp) cc_final: 0.7775 (mmp) REVERT: A 308 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8368 (mtpt) REVERT: A 479 ASN cc_start: 0.7999 (t0) cc_final: 0.7743 (t0) REVERT: B 8 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 323 LYS cc_start: 0.8405 (tttt) cc_final: 0.8173 (tttp) REVERT: B 396 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: B 548 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6870 (ttp-110) REVERT: D 39 THR cc_start: 0.8237 (p) cc_final: 0.7879 (p) REVERT: D 42 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7103 (mtm180) REVERT: C 14 THR cc_start: 0.7918 (p) cc_final: 0.7699 (p) REVERT: C 59 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 85 LYS cc_start: 0.8562 (tppt) cc_final: 0.8269 (tppt) REVERT: E 308 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8318 (mtpt) REVERT: E 479 ASN cc_start: 0.8031 (t0) cc_final: 0.7806 (t0) REVERT: F 8 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7993 (t) REVERT: F 116 MET cc_start: 0.8576 (mmm) cc_final: 0.8206 (mmp) REVERT: F 239 LYS cc_start: 0.8469 (ptmm) cc_final: 0.8149 (tttm) REVERT: F 323 LYS cc_start: 0.8415 (tttt) cc_final: 0.8185 (tttp) REVERT: F 396 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: F 520 ASP cc_start: 0.8176 (t0) cc_final: 0.7657 (m-30) REVERT: F 548 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6849 (ttp-110) REVERT: H 39 THR cc_start: 0.8234 (p) cc_final: 0.7872 (p) REVERT: H 42 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7102 (mtm180) REVERT: G 14 THR cc_start: 0.7875 (p) cc_final: 0.7638 (p) REVERT: G 59 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8478 (tp) outliers start: 47 outliers final: 31 residues processed: 260 average time/residue: 0.1412 time to fit residues: 57.8294 Evaluate side-chains 252 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 182 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 0.0470 chunk 157 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101102 restraints weight = 28097.415| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.79 r_work: 0.2993 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21234 Z= 0.098 Angle : 0.507 8.667 28772 Z= 0.265 Chirality : 0.041 0.179 3256 Planarity : 0.004 0.053 3652 Dihedral : 6.633 92.262 2932 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.74 % Allowed : 13.22 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2582 helix: 2.23 (0.15), residues: 1238 sheet: 0.70 (0.33), residues: 260 loop : -1.48 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.012 0.001 TYR B 510 PHE 0.019 0.001 PHE C 62 TRP 0.007 0.001 TRP B 294 HIS 0.002 0.000 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (21232) covalent geometry : angle 0.50703 / 0.27 (28772) hydrogen bonds : bond 0.03535 / 2.37 ( 985) hydrogen bonds : angle 4.12717 / 2.96 ( 2889) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.812 Fit side-chains REVERT: A 85 LYS cc_start: 0.8566 (tppt) cc_final: 0.8261 (tppt) REVERT: A 308 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8382 (mtpt) REVERT: A 479 ASN cc_start: 0.7995 (t0) cc_final: 0.7790 (t0) REVERT: B 8 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8048 (t) REVERT: B 116 MET cc_start: 0.8547 (mmm) cc_final: 0.8114 (mmm) REVERT: B 239 LYS cc_start: 0.8390 (ptmm) cc_final: 0.8092 (tttm) REVERT: B 323 LYS cc_start: 0.8411 (tttt) cc_final: 0.8185 (tttp) REVERT: B 396 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7646 (pp20) REVERT: B 520 ASP cc_start: 0.8146 (t0) cc_final: 0.7680 (m-30) REVERT: B 548 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6839 (ttp-110) REVERT: D 39 THR cc_start: 0.8387 (p) cc_final: 0.8016 (p) REVERT: D 42 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7048 (mtm180) REVERT: C 59 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8498 (tp) REVERT: E 308 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8304 (mtpt) REVERT: E 479 ASN cc_start: 0.8028 (t0) cc_final: 0.7805 (t0) REVERT: F 8 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8031 (t) REVERT: F 116 MET cc_start: 0.8584 (mmm) cc_final: 0.8253 (mmp) REVERT: F 239 LYS cc_start: 0.8389 (ptmm) cc_final: 0.8097 (tttm) REVERT: F 323 LYS cc_start: 0.8414 (tttt) cc_final: 0.8187 (tttp) REVERT: F 396 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: F 520 ASP cc_start: 0.8157 (t0) cc_final: 0.7664 (m-30) REVERT: H 39 THR cc_start: 0.8383 (p) cc_final: 0.8007 (p) REVERT: H 42 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7087 (mtm180) REVERT: G 59 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8485 (tp) outliers start: 40 outliers final: 27 residues processed: 248 average time/residue: 0.1416 time to fit residues: 55.3610 Evaluate side-chains 246 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101475 restraints weight = 28100.683| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.78 r_work: 0.2982 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21234 Z= 0.100 Angle : 0.505 8.369 28772 Z= 0.266 Chirality : 0.041 0.177 3256 Planarity : 0.004 0.054 3652 Dihedral : 6.592 92.159 2932 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.57 % Allowed : 13.65 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2582 helix: 2.31 (0.15), residues: 1240 sheet: 0.71 (0.33), residues: 260 loop : -1.40 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.013 0.001 TYR B 510 PHE 0.020 0.001 PHE C 62 TRP 0.008 0.001 TRP F 294 HIS 0.003 0.000 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21232) covalent geometry : angle 0.50505 / 0.27 (28772) hydrogen bonds : bond 0.03621 / 2.43 ( 985) hydrogen bonds : angle 4.09507 / 2.93 ( 2889) Misc. bond : bond 0.00038 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.639 Fit side-chains REVERT: A 479 ASN cc_start: 0.7993 (t0) cc_final: 0.7774 (t0) REVERT: B 8 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8001 (t) REVERT: B 116 MET cc_start: 0.8554 (mmm) cc_final: 0.8233 (mmp) REVERT: B 239 LYS cc_start: 0.8383 (ptmm) cc_final: 0.8109 (tttm) REVERT: B 323 LYS cc_start: 0.8416 (tttt) cc_final: 0.8188 (tttp) REVERT: B 396 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: B 520 ASP cc_start: 0.8176 (t0) cc_final: 0.7695 (m-30) REVERT: D 39 THR cc_start: 0.8351 (p) cc_final: 0.7992 (p) REVERT: D 42 ARG cc_start: 0.7550 (ttm110) cc_final: 0.7038 (mtm180) REVERT: C 59 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8435 (tp) REVERT: E 308 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8294 (mtpt) REVERT: E 479 ASN cc_start: 0.8007 (t0) cc_final: 0.7790 (t0) REVERT: F 8 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8038 (t) REVERT: F 116 MET cc_start: 0.8597 (mmm) cc_final: 0.8283 (mmp) REVERT: F 239 LYS cc_start: 0.8347 (ptmm) cc_final: 0.8086 (tttm) REVERT: F 271 ASP cc_start: 0.8197 (t0) cc_final: 0.7942 (t0) REVERT: F 323 LYS cc_start: 0.8401 (tttt) cc_final: 0.8173 (tttp) REVERT: F 396 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: F 520 ASP cc_start: 0.8183 (t0) cc_final: 0.7686 (m-30) REVERT: F 548 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6774 (ttp-110) REVERT: H 39 THR cc_start: 0.8339 (p) cc_final: 0.7974 (p) REVERT: H 42 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7036 (mtm180) REVERT: G 59 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8428 (tp) outliers start: 36 outliers final: 28 residues processed: 236 average time/residue: 0.1378 time to fit residues: 51.1850 Evaluate side-chains 242 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 65 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 177 optimal weight: 0.3980 chunk 217 optimal weight: 10.0000 chunk 161 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS H 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102897 restraints weight = 28131.686| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.80 r_work: 0.3000 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21234 Z= 0.092 Angle : 0.494 10.584 28772 Z= 0.257 Chirality : 0.040 0.179 3256 Planarity : 0.004 0.053 3652 Dihedral : 6.487 91.163 2932 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.65 % Allowed : 13.78 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2582 helix: 2.41 (0.15), residues: 1242 sheet: 0.86 (0.34), residues: 246 loop : -1.26 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.012 0.001 TYR B 510 PHE 0.018 0.001 PHE C 62 TRP 0.008 0.001 TRP F 294 HIS 0.003 0.000 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (21232) covalent geometry : angle 0.49427 / 0.26 (28772) hydrogen bonds : bond 0.03186 / 2.14 ( 985) hydrogen bonds : angle 4.05456 / 2.91 ( 2889) Misc. bond : bond 0.00019 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4887.51 seconds wall clock time: 84 minutes 29.07 seconds (5069.07 seconds total)