Starting phenix.real_space_refine on Thu Feb 5 17:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6p_25723/02_2026/7t6p_25723.cif" } resolution = 2.8 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= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 3.97, per 1000 atoms: 0.20 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.1, 143.1, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 793.5 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 8 sheets defined 65.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.740A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.882A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.653A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.096A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.769A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.917A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.816A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 306 through 309 removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.108A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.826A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 4.388A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.660A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.161A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.575A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.566A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 604 removed outlier: 3.833A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.780A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.881A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.958A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.642A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.573A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.082A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 4.031A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.719A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.556A pdb=" N LEU B 234 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 235' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.825A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 306 through 309 removed outlier: 3.571A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.113A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.815A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 510 removed outlier: 4.132A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.624A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.528A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 604 removed outlier: 3.828A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.706A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.932A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.587A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.531A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.853A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.105A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.601A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.531A pdb=" N LEU C 234 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.001A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.514A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.204A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.682A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.828A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.558A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.648A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 510 removed outlier: 4.028A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.626A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 Processing helix chain 'C' and resid 569 through 604 removed outlier: 4.075A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.742A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.879A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.583A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.098A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.038A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.729A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.550A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 235' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.838A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.085A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.803A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 510 removed outlier: 4.174A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.633A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.551A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 604 removed outlier: 3.849A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.837A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.852A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.809A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.851A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1060 hydrogen bonds defined for protein. 3135 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: 2.77 Time building geometry restraints manager: 2.08 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: 6103 1.34 - 1.46: 3961 1.46 - 1.58: 9568 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.25e+01 bond pdb=" CG1 ILE D 501 " pdb=" CD1 ILE D 501 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.14e+01 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.24e-02 6.50e+03 1.13e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25898 2.49 - 4.97: 819 4.97 - 7.46: 174 7.46 - 9.95: 57 9.95 - 12.44: 16 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C LEU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C LEU A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C LEU B 604 " pdb=" N GLU B 605 " pdb=" CA GLU B 605 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.01e+01 angle pdb=" C VAL C 378 " pdb=" N THR C 379 " pdb=" CA THR C 379 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C PRO B 362 " pdb=" N ARG B 363 " pdb=" CA ARG B 363 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 10391 15.92 - 31.84: 1060 31.84 - 47.75: 274 47.75 - 63.67: 59 63.67 - 79.59: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE A 510 " pdb=" C ILE A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 146.06 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" CA ILE C 510 " pdb=" C ILE C 510 " pdb=" N THR C 511 " pdb=" CA THR C 511 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA THR D 514 " pdb=" C THR D 514 " pdb=" N GLU D 515 " pdb=" CA GLU D 515 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2699 0.088 - 0.175: 327 0.175 - 0.263: 32 0.263 - 0.350: 8 0.350 - 0.438: 6 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB THR C 379 " pdb=" CA THR C 379 " pdb=" OG1 THR C 379 " pdb=" CG2 THR C 379 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB THR A 379 " pdb=" CA THR A 379 " pdb=" OG1 THR A 379 " pdb=" CG2 THR A 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB THR B 379 " pdb=" CA THR B 379 " pdb=" OG1 THR B 379 " pdb=" CG2 THR B 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C THR D 511 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 512 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 585 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C VAL D 585 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL D 585 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 586 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C THR B 511 " 0.047 2.00e-02 2.50e+03 pdb=" O THR B 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 512 " -0.016 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5711 2.83 - 3.35: 17920 3.35 - 3.86: 33109 3.86 - 4.38: 39220 4.38 - 4.90: 65697 Nonbonded interactions: 161657 Sorted by model distance: nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.310 3.040 nonbonded pdb=" O LEU C 568 " pdb=" ND2 ASN C 572 " model vdw 2.368 3.120 nonbonded pdb=" O LEU D 568 " pdb=" ND2 ASN D 572 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 73 " pdb=" NH1 ARG A 75 " model vdw 2.379 3.120 nonbonded pdb=" O LEU B 218 " pdb=" OG SER B 221 " model vdw 2.379 3.040 ... (remaining 161652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.005 0.132 19860 Z= 0.273 Angle : 1.127 12.437 26964 Z= 0.596 Chirality : 0.061 0.438 3072 Planarity : 0.008 0.067 3416 Dihedral : 14.543 79.591 7236 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.37 (0.13), residues: 2408 helix: -2.24 (0.10), residues: 1444 sheet: -1.71 (0.51), residues: 64 loop : -1.97 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 359 TYR 0.039 0.002 TYR A 328 PHE 0.029 0.003 PHE C 456 TRP 0.017 0.002 TRP B 583 HIS 0.008 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00531 (19860) covalent geometry : angle 1.12704 (26964) hydrogen bonds : bond 0.15518 ( 1060) hydrogen bonds : angle 7.10612 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7494 (tp-100) REVERT: A 55 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 257 GLN cc_start: 0.7004 (mm110) cc_final: 0.6578 (tp40) REVERT: A 497 MET cc_start: 0.7923 (ttt) cc_final: 0.7676 (ttt) REVERT: A 515 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6113 (mm-30) REVERT: A 583 TRP cc_start: 0.8131 (p-90) cc_final: 0.7877 (p-90) REVERT: B 51 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7467 (tp-100) REVERT: B 55 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 257 GLN cc_start: 0.7030 (mm110) cc_final: 0.6720 (mm110) REVERT: B 429 ILE cc_start: 0.7628 (mt) cc_final: 0.7377 (tp) REVERT: B 447 MET cc_start: 0.7461 (mtm) cc_final: 0.7190 (ptm) REVERT: C 51 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7482 (tp-100) REVERT: C 55 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7652 (mt-10) REVERT: C 181 LEU cc_start: 0.8399 (tt) cc_final: 0.8170 (tm) REVERT: C 239 GLN cc_start: 0.8047 (tt0) cc_final: 0.7828 (tt0) REVERT: D 257 GLN cc_start: 0.7158 (mm110) cc_final: 0.6939 (mm110) REVERT: D 260 MET cc_start: 0.7342 (mmp) cc_final: 0.7080 (mmt) REVERT: D 447 MET cc_start: 0.7485 (mtm) cc_final: 0.7242 (ptm) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.5269 time to fit residues: 247.0526 Evaluate side-chains 316 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN A 380 HIS A 635 ASN B 31 GLN B 185 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN B 380 HIS B 635 ASN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 374 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 369 GLN D 374 GLN D 380 HIS D 635 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124789 restraints weight = 23946.190| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.38 r_work: 0.3389 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19860 Z= 0.126 Angle : 0.612 9.485 26964 Z= 0.316 Chirality : 0.041 0.247 3072 Planarity : 0.005 0.046 3416 Dihedral : 4.920 25.656 2644 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.24 % Allowed : 10.54 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.37 (0.15), residues: 2408 helix: -0.22 (0.13), residues: 1456 sheet: -2.06 (0.47), residues: 84 loop : -1.87 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 305 TYR 0.020 0.001 TYR B 555 PHE 0.021 0.001 PHE B 611 TRP 0.008 0.001 TRP C 462 HIS 0.003 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00275 (19860) covalent geometry : angle 0.61250 (26964) hydrogen bonds : bond 0.04048 ( 1060) hydrogen bonds : angle 4.44615 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 351 time to evaluate : 0.710 Fit side-chains REVERT: A 55 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 214 GLN cc_start: 0.7600 (mp10) cc_final: 0.7012 (mp10) REVERT: A 381 GLN cc_start: 0.6879 (mp10) cc_final: 0.5974 (mt0) REVERT: A 487 PHE cc_start: 0.7413 (m-10) cc_final: 0.7151 (m-10) REVERT: A 497 MET cc_start: 0.7527 (ttt) cc_final: 0.7272 (ttt) REVERT: B 51 GLN cc_start: 0.7478 (tp-100) cc_final: 0.7277 (tp-100) REVERT: B 55 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7526 (mt-10) REVERT: B 214 GLN cc_start: 0.7378 (mp10) cc_final: 0.6950 (mp10) REVERT: B 294 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7207 (pt0) REVERT: B 349 TYR cc_start: 0.8240 (m-80) cc_final: 0.7992 (m-80) REVERT: B 380 HIS cc_start: 0.6913 (t-170) cc_final: 0.6713 (t70) REVERT: B 381 GLN cc_start: 0.6909 (mp10) cc_final: 0.5986 (mt0) REVERT: B 487 PHE cc_start: 0.7464 (m-10) cc_final: 0.7195 (m-10) REVERT: C 51 GLN cc_start: 0.7549 (tp-100) cc_final: 0.7259 (tp-100) REVERT: C 55 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7449 (mt-10) REVERT: C 62 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7452 (mttt) REVERT: C 214 GLN cc_start: 0.7523 (mp10) cc_final: 0.6962 (mp10) REVERT: C 215 MET cc_start: 0.8401 (mmm) cc_final: 0.8141 (tpp) REVERT: C 222 TYR cc_start: 0.6834 (m-80) cc_final: 0.6320 (m-80) REVERT: C 257 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6565 (mm110) REVERT: C 372 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6505 (mt) REVERT: C 487 PHE cc_start: 0.7352 (m-10) cc_final: 0.7132 (m-10) REVERT: C 497 MET cc_start: 0.7469 (ttt) cc_final: 0.7180 (ttt) REVERT: D 55 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7693 (mt-10) REVERT: D 214 GLN cc_start: 0.7376 (mp10) cc_final: 0.6950 (mp10) REVERT: D 294 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 315 GLU cc_start: 0.7789 (mp0) cc_final: 0.7565 (mp0) REVERT: D 381 GLN cc_start: 0.6930 (mp10) cc_final: 0.6007 (mt0) REVERT: D 487 PHE cc_start: 0.7410 (m-10) cc_final: 0.7185 (m-10) outliers start: 47 outliers final: 7 residues processed: 368 average time/residue: 0.5077 time to fit residues: 213.1890 Evaluate side-chains 305 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 297 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 131 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 261 GLN A 310 GLN A 380 HIS B 73 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN B 310 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 374 GLN C 418 GLN D 73 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 310 GLN D 380 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114985 restraints weight = 23636.230| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.44 r_work: 0.3213 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19860 Z= 0.155 Angle : 0.602 11.004 26964 Z= 0.310 Chirality : 0.041 0.221 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.737 26.779 2644 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.19 % Allowed : 14.89 % Favored : 82.92 % 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: -0.59 (0.16), residues: 2408 helix: 0.45 (0.13), residues: 1484 sheet: -1.53 (0.45), residues: 96 loop : -1.73 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.014 0.001 TYR C 555 PHE 0.011 0.001 PHE C 523 TRP 0.008 0.001 TRP C 583 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00364 (19860) covalent geometry : angle 0.60160 (26964) hydrogen bonds : bond 0.04086 ( 1060) hydrogen bonds : angle 4.24812 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 0.679 Fit side-chains REVERT: A 55 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 214 GLN cc_start: 0.7462 (mp10) cc_final: 0.6856 (mp10) REVERT: A 257 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6578 (mm110) REVERT: A 315 GLU cc_start: 0.7810 (mp0) cc_final: 0.7244 (mp0) REVERT: A 349 TYR cc_start: 0.8103 (m-80) cc_final: 0.7832 (m-80) REVERT: A 381 GLN cc_start: 0.6761 (mp10) cc_final: 0.5845 (mt0) REVERT: A 429 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6685 (tp) REVERT: A 487 PHE cc_start: 0.7424 (m-10) cc_final: 0.7189 (m-10) REVERT: A 497 MET cc_start: 0.7201 (ttt) cc_final: 0.6896 (ttt) REVERT: B 55 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 99 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.5192 (mpp) REVERT: B 214 GLN cc_start: 0.7368 (mp10) cc_final: 0.6766 (mp10) REVERT: B 217 ASN cc_start: 0.7603 (m-40) cc_final: 0.7401 (m-40) REVERT: B 257 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6429 (mm110) REVERT: B 260 MET cc_start: 0.6826 (mmt) cc_final: 0.6493 (mmt) REVERT: B 315 GLU cc_start: 0.7911 (mp0) cc_final: 0.7328 (mp0) REVERT: B 349 TYR cc_start: 0.8122 (m-80) cc_final: 0.7785 (m-80) REVERT: B 381 GLN cc_start: 0.6879 (mp10) cc_final: 0.6022 (mt0) REVERT: B 487 PHE cc_start: 0.7418 (m-10) cc_final: 0.7176 (m-10) REVERT: C 55 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7422 (mt-10) REVERT: C 62 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7504 (mttt) REVERT: C 214 GLN cc_start: 0.7477 (mp10) cc_final: 0.6848 (mp10) REVERT: C 215 MET cc_start: 0.8274 (mmm) cc_final: 0.7953 (tpp) REVERT: C 315 GLU cc_start: 0.7843 (mp0) cc_final: 0.7255 (mp0) REVERT: C 487 PHE cc_start: 0.7503 (m-10) cc_final: 0.7292 (m-10) REVERT: C 497 MET cc_start: 0.7373 (ttt) cc_final: 0.7050 (ttt) REVERT: D 55 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 99 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.5373 (mpp) REVERT: D 214 GLN cc_start: 0.7409 (mp10) cc_final: 0.6784 (mp10) REVERT: D 217 ASN cc_start: 0.7609 (m-40) cc_final: 0.7402 (m-40) REVERT: D 315 GLU cc_start: 0.7823 (mp0) cc_final: 0.7206 (mp0) REVERT: D 349 TYR cc_start: 0.8127 (m-80) cc_final: 0.7817 (m-80) REVERT: D 372 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6656 (mt) REVERT: D 381 GLN cc_start: 0.6843 (mp10) cc_final: 0.5975 (mt0) outliers start: 46 outliers final: 6 residues processed: 344 average time/residue: 0.6037 time to fit residues: 234.6457 Evaluate side-chains 290 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 280 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 372 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN A 380 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 310 GLN C 370 GLN C 418 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 261 GLN D 310 GLN D 380 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116665 restraints weight = 23314.361| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.41 r_work: 0.3234 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19860 Z= 0.119 Angle : 0.575 10.077 26964 Z= 0.292 Chirality : 0.041 0.321 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.504 27.357 2644 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.81 % Allowed : 16.22 % Favored : 80.96 % 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: -0.05 (0.17), residues: 2408 helix: 0.91 (0.14), residues: 1476 sheet: -1.91 (0.44), residues: 104 loop : -1.46 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 43 TYR 0.013 0.001 TYR D 555 PHE 0.008 0.001 PHE D 537 TRP 0.010 0.001 TRP B 583 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00265 (19860) covalent geometry : angle 0.57504 (26964) hydrogen bonds : bond 0.03696 ( 1060) hydrogen bonds : angle 4.09127 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 0.708 Fit side-chains REVERT: A 55 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 214 GLN cc_start: 0.7522 (mp10) cc_final: 0.6841 (mp10) REVERT: A 257 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6542 (mm110) REVERT: A 294 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 315 GLU cc_start: 0.7802 (mp0) cc_final: 0.7189 (mp0) REVERT: A 318 SER cc_start: 0.7736 (m) cc_final: 0.7407 (t) REVERT: A 349 TYR cc_start: 0.8105 (m-80) cc_final: 0.7795 (m-80) REVERT: A 372 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6553 (mt) REVERT: A 380 HIS cc_start: 0.6953 (t-170) cc_final: 0.6731 (t70) REVERT: A 381 GLN cc_start: 0.6642 (mp10) cc_final: 0.5675 (mt0) REVERT: A 487 PHE cc_start: 0.7439 (m-10) cc_final: 0.7188 (m-10) REVERT: A 497 MET cc_start: 0.7112 (ttt) cc_final: 0.6878 (ttt) REVERT: A 528 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7091 (p) REVERT: B 55 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7673 (mt-10) REVERT: B 214 GLN cc_start: 0.7404 (mp10) cc_final: 0.6774 (mp10) REVERT: B 217 ASN cc_start: 0.7649 (m-40) cc_final: 0.7411 (m-40) REVERT: B 257 GLN cc_start: 0.6622 (mm-40) cc_final: 0.6337 (mm110) REVERT: B 315 GLU cc_start: 0.7804 (mp0) cc_final: 0.7196 (mp0) REVERT: B 349 TYR cc_start: 0.8096 (m-80) cc_final: 0.7798 (m-80) REVERT: B 372 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6678 (mt) REVERT: B 381 GLN cc_start: 0.6753 (mp10) cc_final: 0.5839 (mt0) REVERT: B 487 PHE cc_start: 0.7464 (m-10) cc_final: 0.7219 (m-10) REVERT: B 528 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7015 (p) REVERT: C 62 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7476 (mttt) REVERT: C 214 GLN cc_start: 0.7478 (mp10) cc_final: 0.6781 (mp10) REVERT: C 215 MET cc_start: 0.8225 (mmm) cc_final: 0.7853 (tpp) REVERT: C 294 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7126 (mt-10) REVERT: C 315 GLU cc_start: 0.7748 (mp0) cc_final: 0.7168 (mp0) REVERT: C 318 SER cc_start: 0.7738 (m) cc_final: 0.7400 (t) REVERT: C 497 MET cc_start: 0.7279 (ttt) cc_final: 0.6977 (ttt) REVERT: C 528 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7081 (p) REVERT: D 55 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7492 (mt-10) REVERT: D 214 GLN cc_start: 0.7357 (mp10) cc_final: 0.6722 (mp10) REVERT: D 217 ASN cc_start: 0.7657 (m-40) cc_final: 0.7405 (m-40) REVERT: D 257 GLN cc_start: 0.6646 (mm-40) cc_final: 0.6367 (mm110) REVERT: D 315 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: D 318 SER cc_start: 0.7764 (m) cc_final: 0.7420 (t) REVERT: D 349 TYR cc_start: 0.8097 (m-80) cc_final: 0.7813 (m-80) REVERT: D 372 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6695 (mt) REVERT: D 380 HIS cc_start: 0.6967 (t-170) cc_final: 0.6748 (t70) REVERT: D 381 GLN cc_start: 0.6647 (mp10) cc_final: 0.5680 (mt0) REVERT: D 528 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7019 (p) outliers start: 59 outliers final: 20 residues processed: 327 average time/residue: 0.5604 time to fit residues: 207.7919 Evaluate side-chains 302 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.0030 chunk 109 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN C 51 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 418 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121089 restraints weight = 23533.266| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.32 r_work: 0.3341 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19860 Z= 0.110 Angle : 0.558 11.018 26964 Z= 0.282 Chirality : 0.040 0.296 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.372 27.760 2644 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.39 % Allowed : 17.80 % Favored : 79.82 % 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: 0.34 (0.17), residues: 2408 helix: 1.22 (0.14), residues: 1480 sheet: -1.90 (0.44), residues: 104 loop : -1.30 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.013 0.001 TYR B 555 PHE 0.008 0.001 PHE B 537 TRP 0.010 0.001 TRP A 583 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00240 (19860) covalent geometry : angle 0.55835 (26964) hydrogen bonds : bond 0.03539 ( 1060) hydrogen bonds : angle 3.98747 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.708 Fit side-chains REVERT: A 31 GLN cc_start: 0.6972 (pt0) cc_final: 0.6394 (pp30) REVERT: A 55 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 99 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.5405 (mpp) REVERT: A 214 GLN cc_start: 0.7566 (mp10) cc_final: 0.6822 (mp10) REVERT: A 257 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6735 (mm110) REVERT: A 294 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 315 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 318 SER cc_start: 0.7880 (m) cc_final: 0.7577 (t) REVERT: A 349 TYR cc_start: 0.8262 (m-80) cc_final: 0.7969 (m-80) REVERT: A 372 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6732 (mt) REVERT: A 380 HIS cc_start: 0.6940 (t-170) cc_final: 0.6732 (t70) REVERT: A 381 GLN cc_start: 0.6694 (mp10) cc_final: 0.5713 (mt0) REVERT: A 447 MET cc_start: 0.7485 (ptm) cc_final: 0.7260 (ptp) REVERT: A 487 PHE cc_start: 0.7591 (m-10) cc_final: 0.7390 (m-10) REVERT: A 497 MET cc_start: 0.7253 (ttt) cc_final: 0.7023 (ttt) REVERT: A 528 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7310 (p) REVERT: B 55 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 214 GLN cc_start: 0.7611 (mp10) cc_final: 0.6956 (mp10) REVERT: B 257 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6565 (mm110) REVERT: B 315 GLU cc_start: 0.8026 (mp0) cc_final: 0.7405 (mp0) REVERT: B 318 SER cc_start: 0.7960 (m) cc_final: 0.7641 (t) REVERT: B 349 TYR cc_start: 0.8245 (m-80) cc_final: 0.7949 (m-80) REVERT: B 381 GLN cc_start: 0.6768 (mp10) cc_final: 0.5811 (mt0) REVERT: B 487 PHE cc_start: 0.7649 (m-10) cc_final: 0.7400 (m-10) REVERT: B 528 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7175 (p) REVERT: C 62 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7609 (mttt) REVERT: C 214 GLN cc_start: 0.7547 (mp10) cc_final: 0.6796 (mp10) REVERT: C 215 MET cc_start: 0.8424 (mmm) cc_final: 0.8105 (tpp) REVERT: C 294 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7281 (mt-10) REVERT: C 315 GLU cc_start: 0.7746 (mp0) cc_final: 0.7304 (mp0) REVERT: C 318 SER cc_start: 0.7986 (m) cc_final: 0.7660 (t) REVERT: C 497 MET cc_start: 0.7435 (ttt) cc_final: 0.7083 (ttt) REVERT: C 501 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7802 (mp) REVERT: C 528 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7241 (p) REVERT: D 31 GLN cc_start: 0.6969 (pt0) cc_final: 0.6367 (pp30) REVERT: D 55 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 99 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.5638 (mpp) REVERT: D 214 GLN cc_start: 0.7561 (mp10) cc_final: 0.6839 (mp10) REVERT: D 257 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6591 (mm110) REVERT: D 315 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: D 318 SER cc_start: 0.7943 (m) cc_final: 0.7606 (t) REVERT: D 349 TYR cc_start: 0.8243 (m-80) cc_final: 0.7968 (m-80) REVERT: D 528 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7227 (p) outliers start: 50 outliers final: 19 residues processed: 328 average time/residue: 0.5522 time to fit residues: 204.9051 Evaluate side-chains 307 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.5980 chunk 174 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 72 optimal weight: 0.0070 chunk 207 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 374 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 380 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120419 restraints weight = 23593.495| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.30 r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19860 Z= 0.113 Angle : 0.568 11.501 26964 Z= 0.284 Chirality : 0.040 0.230 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.311 27.551 2644 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.29 % Allowed : 18.94 % Favored : 78.77 % 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: 0.43 (0.17), residues: 2408 helix: 1.25 (0.14), residues: 1488 sheet: -1.89 (0.44), residues: 104 loop : -1.18 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.012 0.001 TYR B 555 PHE 0.008 0.001 PHE B 537 TRP 0.010 0.001 TRP A 583 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00253 (19860) covalent geometry : angle 0.56815 (26964) hydrogen bonds : bond 0.03519 ( 1060) hydrogen bonds : angle 3.98757 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 0.699 Fit side-chains REVERT: A 31 GLN cc_start: 0.6942 (pt0) cc_final: 0.6390 (pp30) REVERT: A 55 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 100 GLU cc_start: 0.7772 (pt0) cc_final: 0.7563 (pt0) REVERT: A 214 GLN cc_start: 0.7592 (mp10) cc_final: 0.6786 (mp10) REVERT: A 257 GLN cc_start: 0.7031 (mm-40) cc_final: 0.6753 (mm110) REVERT: A 294 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 315 GLU cc_start: 0.7890 (mp0) cc_final: 0.7357 (mp0) REVERT: A 318 SER cc_start: 0.7904 (m) cc_final: 0.7626 (t) REVERT: A 349 TYR cc_start: 0.8236 (m-80) cc_final: 0.7919 (m-80) REVERT: A 381 GLN cc_start: 0.6793 (mp10) cc_final: 0.5857 (mt0) REVERT: A 429 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6864 (tp) REVERT: A 447 MET cc_start: 0.7476 (ptm) cc_final: 0.7232 (ptp) REVERT: A 528 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7277 (p) REVERT: B 55 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 214 GLN cc_start: 0.7524 (mp10) cc_final: 0.6845 (mp10) REVERT: B 315 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: B 318 SER cc_start: 0.8058 (m) cc_final: 0.7757 (t) REVERT: B 349 TYR cc_start: 0.8216 (m-80) cc_final: 0.7898 (m-80) REVERT: B 372 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6824 (mt) REVERT: B 381 GLN cc_start: 0.6847 (mp10) cc_final: 0.5915 (mt0) REVERT: B 528 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7135 (p) REVERT: C 31 GLN cc_start: 0.6979 (pt0) cc_final: 0.6391 (pp30) REVERT: C 62 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7608 (mttt) REVERT: C 214 GLN cc_start: 0.7582 (mp10) cc_final: 0.6776 (mp10) REVERT: C 215 MET cc_start: 0.8427 (mmm) cc_final: 0.8113 (tpp) REVERT: C 294 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 315 GLU cc_start: 0.7744 (mp0) cc_final: 0.7254 (mp0) REVERT: C 318 SER cc_start: 0.8024 (m) cc_final: 0.7672 (t) REVERT: C 418 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: C 447 MET cc_start: 0.7519 (ptm) cc_final: 0.7246 (ptp) REVERT: C 497 MET cc_start: 0.7454 (ttt) cc_final: 0.7125 (ttt) REVERT: C 501 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 528 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7214 (p) REVERT: D 31 GLN cc_start: 0.6887 (pt0) cc_final: 0.6356 (pp30) REVERT: D 55 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 100 GLU cc_start: 0.7795 (pt0) cc_final: 0.7589 (pt0) REVERT: D 214 GLN cc_start: 0.7484 (mp10) cc_final: 0.6798 (mp10) REVERT: D 257 GLN cc_start: 0.6907 (mm-40) cc_final: 0.6536 (mm110) REVERT: D 315 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: D 318 SER cc_start: 0.7936 (m) cc_final: 0.7618 (t) REVERT: D 349 TYR cc_start: 0.8256 (m-80) cc_final: 0.7915 (m-80) REVERT: D 429 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6717 (tp) REVERT: D 447 MET cc_start: 0.7711 (mtp) cc_final: 0.7159 (ttm) REVERT: D 528 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7176 (p) outliers start: 48 outliers final: 18 residues processed: 318 average time/residue: 0.5802 time to fit residues: 208.3925 Evaluate side-chains 294 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 0.0670 chunk 175 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 192 optimal weight: 0.0070 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 310 GLN B 374 GLN C 51 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 374 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118259 restraints weight = 23565.495| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.36 r_work: 0.3305 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19860 Z= 0.126 Angle : 0.582 12.118 26964 Z= 0.290 Chirality : 0.041 0.218 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.316 27.625 2644 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.58 % Allowed : 19.51 % Favored : 77.91 % 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: 0.52 (0.18), residues: 2408 helix: 1.30 (0.14), residues: 1488 sheet: -1.90 (0.44), residues: 104 loop : -1.09 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 414 TYR 0.013 0.001 TYR D 555 PHE 0.009 0.001 PHE B 537 TRP 0.010 0.001 TRP C 583 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00292 (19860) covalent geometry : angle 0.58168 (26964) hydrogen bonds : bond 0.03651 ( 1060) hydrogen bonds : angle 4.00774 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 0.718 Fit side-chains REVERT: A 38 MET cc_start: 0.8175 (mmm) cc_final: 0.7941 (tpp) REVERT: A 55 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 214 GLN cc_start: 0.7514 (mp10) cc_final: 0.6752 (mp10) REVERT: A 294 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 315 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 318 SER cc_start: 0.7887 (m) cc_final: 0.7593 (t) REVERT: A 349 TYR cc_start: 0.8225 (m-80) cc_final: 0.7890 (m-80) REVERT: A 381 GLN cc_start: 0.6662 (mp10) cc_final: 0.5855 (mt0) REVERT: A 429 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6814 (tp) REVERT: A 447 MET cc_start: 0.7416 (ptm) cc_final: 0.7199 (ptp) REVERT: A 528 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7172 (p) REVERT: B 55 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 214 GLN cc_start: 0.7468 (mp10) cc_final: 0.6756 (mp10) REVERT: B 315 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 318 SER cc_start: 0.8020 (m) cc_final: 0.7720 (t) REVERT: B 349 TYR cc_start: 0.8165 (m-80) cc_final: 0.7877 (m-80) REVERT: B 372 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6821 (mt) REVERT: B 379 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7790 (p) REVERT: B 381 GLN cc_start: 0.6785 (mp10) cc_final: 0.5998 (mt0) REVERT: B 447 MET cc_start: 0.7434 (mtp) cc_final: 0.7031 (ttm) REVERT: B 528 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7046 (p) REVERT: C 62 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7594 (mttt) REVERT: C 214 GLN cc_start: 0.7615 (mp10) cc_final: 0.7169 (mp10) REVERT: C 215 MET cc_start: 0.8374 (mmm) cc_final: 0.8066 (tpp) REVERT: C 294 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7329 (mt-10) REVERT: C 315 GLU cc_start: 0.7616 (mp0) cc_final: 0.7163 (mp0) REVERT: C 318 SER cc_start: 0.7822 (m) cc_final: 0.7518 (t) REVERT: C 418 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: C 447 MET cc_start: 0.7483 (ptm) cc_final: 0.7182 (ptp) REVERT: C 497 MET cc_start: 0.7335 (ttt) cc_final: 0.6971 (ttt) REVERT: C 501 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7643 (mp) REVERT: C 528 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7121 (p) REVERT: D 31 GLN cc_start: 0.6837 (pt0) cc_final: 0.6324 (pp30) REVERT: D 55 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7806 (mt-10) REVERT: D 99 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.5537 (mpp) REVERT: D 214 GLN cc_start: 0.7386 (mp10) cc_final: 0.6735 (mp10) REVERT: D 257 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6413 (mm110) REVERT: D 315 GLU cc_start: 0.7844 (mp0) cc_final: 0.7296 (mp0) REVERT: D 318 SER cc_start: 0.7901 (m) cc_final: 0.7591 (t) REVERT: D 349 TYR cc_start: 0.8179 (m-80) cc_final: 0.7903 (m-80) REVERT: D 379 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7794 (p) REVERT: D 381 GLN cc_start: 0.6579 (mp10) cc_final: 0.5813 (mt0) REVERT: D 429 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6670 (tp) REVERT: D 447 MET cc_start: 0.7550 (mtp) cc_final: 0.7055 (ttm) REVERT: D 528 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7061 (p) outliers start: 54 outliers final: 19 residues processed: 312 average time/residue: 0.5508 time to fit residues: 195.0419 Evaluate side-chains 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 310 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117852 restraints weight = 23590.149| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.36 r_work: 0.3298 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19860 Z= 0.127 Angle : 0.594 13.002 26964 Z= 0.294 Chirality : 0.041 0.236 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.317 27.550 2644 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.43 % Allowed : 19.70 % Favored : 77.86 % 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: 0.47 (0.18), residues: 2408 helix: 1.24 (0.14), residues: 1484 sheet: -1.89 (0.44), residues: 104 loop : -1.06 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 414 TYR 0.013 0.001 TYR D 555 PHE 0.009 0.001 PHE A 537 TRP 0.011 0.001 TRP C 286 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00294 (19860) covalent geometry : angle 0.59363 (26964) hydrogen bonds : bond 0.03678 ( 1060) hydrogen bonds : angle 4.04663 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.767 Fit side-chains REVERT: A 55 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 176 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7272 (tt0) REVERT: A 214 GLN cc_start: 0.7596 (mp10) cc_final: 0.6870 (mp10) REVERT: A 294 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 315 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 318 SER cc_start: 0.7935 (m) cc_final: 0.7652 (t) REVERT: A 349 TYR cc_start: 0.8250 (m-80) cc_final: 0.7922 (m-80) REVERT: A 381 GLN cc_start: 0.6793 (mp10) cc_final: 0.5820 (mt0) REVERT: A 429 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6873 (tp) REVERT: A 447 MET cc_start: 0.7578 (ptm) cc_final: 0.7353 (ptp) REVERT: A 528 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7256 (p) REVERT: B 55 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 214 GLN cc_start: 0.7450 (mp10) cc_final: 0.6767 (mp10) REVERT: B 315 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 318 SER cc_start: 0.8075 (m) cc_final: 0.7783 (t) REVERT: B 349 TYR cc_start: 0.8204 (m-80) cc_final: 0.7907 (m-80) REVERT: B 372 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6858 (mt) REVERT: B 379 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7825 (p) REVERT: B 381 GLN cc_start: 0.6810 (mp10) cc_final: 0.6021 (mt0) REVERT: B 447 MET cc_start: 0.7470 (mtp) cc_final: 0.7122 (ttm) REVERT: B 528 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7126 (p) REVERT: C 62 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7607 (mttt) REVERT: C 97 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7059 (mm) REVERT: C 99 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.5769 (mpp) REVERT: C 214 GLN cc_start: 0.7635 (mp10) cc_final: 0.7180 (mp10) REVERT: C 215 MET cc_start: 0.8445 (mmm) cc_final: 0.8131 (tpp) REVERT: C 294 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7390 (mt-10) REVERT: C 315 GLU cc_start: 0.7730 (mp0) cc_final: 0.7269 (mp0) REVERT: C 318 SER cc_start: 0.7932 (m) cc_final: 0.7645 (t) REVERT: C 418 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: C 447 MET cc_start: 0.7562 (ptm) cc_final: 0.7259 (ptp) REVERT: C 497 MET cc_start: 0.7437 (ttt) cc_final: 0.7065 (ttt) REVERT: C 501 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7728 (mp) REVERT: C 528 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7198 (p) REVERT: D 31 GLN cc_start: 0.6954 (pt0) cc_final: 0.6437 (pp30) REVERT: D 55 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7831 (mt-10) REVERT: D 214 GLN cc_start: 0.7410 (mp10) cc_final: 0.6751 (mp10) REVERT: D 315 GLU cc_start: 0.7930 (mp0) cc_final: 0.7371 (mp0) REVERT: D 318 SER cc_start: 0.7950 (m) cc_final: 0.7643 (t) REVERT: D 349 TYR cc_start: 0.8217 (m-80) cc_final: 0.7933 (m-80) REVERT: D 379 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7804 (p) REVERT: D 381 GLN cc_start: 0.6657 (mp10) cc_final: 0.5889 (mt0) REVERT: D 429 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6752 (tp) REVERT: D 447 MET cc_start: 0.7545 (mtp) cc_final: 0.7102 (ttm) REVERT: D 528 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7144 (p) outliers start: 51 outliers final: 24 residues processed: 305 average time/residue: 0.5263 time to fit residues: 182.0178 Evaluate side-chains 301 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 209 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 229 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 310 GLN D 380 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118297 restraints weight = 23463.548| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.35 r_work: 0.3307 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19860 Z= 0.121 Angle : 0.586 12.649 26964 Z= 0.290 Chirality : 0.041 0.232 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.299 27.520 2644 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.67 % Allowed : 19.51 % Favored : 77.81 % 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: 0.52 (0.18), residues: 2408 helix: 1.27 (0.14), residues: 1484 sheet: -1.87 (0.44), residues: 104 loop : -1.02 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 414 TYR 0.013 0.001 TYR C 328 PHE 0.008 0.001 PHE A 537 TRP 0.011 0.001 TRP D 286 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00276 (19860) covalent geometry : angle 0.58577 (26964) hydrogen bonds : bond 0.03616 ( 1060) hydrogen bonds : angle 4.03637 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.765 Fit side-chains REVERT: A 55 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 176 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7262 (tt0) REVERT: A 214 GLN cc_start: 0.7621 (mp10) cc_final: 0.7325 (mp10) REVERT: A 257 GLN cc_start: 0.6440 (tp40) cc_final: 0.6114 (mm110) REVERT: A 294 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 315 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 318 SER cc_start: 0.7879 (m) cc_final: 0.7600 (t) REVERT: A 349 TYR cc_start: 0.8216 (m-80) cc_final: 0.7873 (m-80) REVERT: A 381 GLN cc_start: 0.6708 (mp10) cc_final: 0.5651 (mt0) REVERT: A 429 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6817 (tp) REVERT: A 447 MET cc_start: 0.7506 (ptm) cc_final: 0.7284 (ptp) REVERT: A 528 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 55 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 214 GLN cc_start: 0.7410 (mp10) cc_final: 0.6740 (mp10) REVERT: B 315 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 318 SER cc_start: 0.7998 (m) cc_final: 0.7727 (t) REVERT: B 349 TYR cc_start: 0.8180 (m-80) cc_final: 0.7877 (m-80) REVERT: B 372 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6774 (mt) REVERT: B 379 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7869 (p) REVERT: B 381 GLN cc_start: 0.6738 (mp10) cc_final: 0.5905 (mt0) REVERT: B 447 MET cc_start: 0.7427 (mtp) cc_final: 0.7096 (ttm) REVERT: B 528 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7070 (p) REVERT: C 46 ASP cc_start: 0.7890 (m-30) cc_final: 0.7466 (m-30) REVERT: C 62 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7574 (mttt) REVERT: C 97 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7071 (mm) REVERT: C 99 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.5841 (mpp) REVERT: C 214 GLN cc_start: 0.7622 (mp10) cc_final: 0.7148 (mp10) REVERT: C 215 MET cc_start: 0.8398 (mmm) cc_final: 0.8090 (tpp) REVERT: C 294 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 315 GLU cc_start: 0.7624 (mp0) cc_final: 0.7180 (mp0) REVERT: C 318 SER cc_start: 0.7859 (m) cc_final: 0.7586 (t) REVERT: C 418 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: C 429 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6667 (tp) REVERT: C 447 MET cc_start: 0.7568 (ptm) cc_final: 0.7277 (ptp) REVERT: C 497 MET cc_start: 0.7402 (ttt) cc_final: 0.7035 (ttt) REVERT: C 501 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7705 (mp) REVERT: C 528 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7142 (p) REVERT: D 55 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 214 GLN cc_start: 0.7396 (mp10) cc_final: 0.6729 (mp10) REVERT: D 315 GLU cc_start: 0.7873 (mp0) cc_final: 0.7315 (mp0) REVERT: D 318 SER cc_start: 0.7955 (m) cc_final: 0.7646 (t) REVERT: D 349 TYR cc_start: 0.8174 (m-80) cc_final: 0.7879 (m-80) REVERT: D 379 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7850 (p) REVERT: D 381 GLN cc_start: 0.6597 (mp10) cc_final: 0.5819 (mt0) REVERT: D 429 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6688 (tp) REVERT: D 447 MET cc_start: 0.7593 (mtp) cc_final: 0.7111 (ttm) REVERT: D 528 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7104 (p) outliers start: 56 outliers final: 22 residues processed: 315 average time/residue: 0.5586 time to fit residues: 199.3742 Evaluate side-chains 302 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 123 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 380 HIS ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 370 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 380 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117607 restraints weight = 23570.584| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.36 r_work: 0.3296 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19860 Z= 0.128 Angle : 0.601 12.849 26964 Z= 0.297 Chirality : 0.041 0.233 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.311 27.513 2644 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.15 % Allowed : 20.23 % Favored : 77.62 % 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: 0.53 (0.18), residues: 2408 helix: 1.27 (0.14), residues: 1484 sheet: -1.88 (0.44), residues: 104 loop : -0.98 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 414 TYR 0.015 0.001 TYR D 328 PHE 0.008 0.001 PHE A 537 TRP 0.011 0.001 TRP A 286 HIS 0.003 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00296 (19860) covalent geometry : angle 0.60059 (26964) hydrogen bonds : bond 0.03698 ( 1060) hydrogen bonds : angle 4.06323 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.807 Fit side-chains REVERT: A 55 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 176 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7311 (tt0) REVERT: A 214 GLN cc_start: 0.7582 (mp10) cc_final: 0.7277 (mp10) REVERT: A 257 GLN cc_start: 0.6456 (tp40) cc_final: 0.6118 (mm110) REVERT: A 294 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 315 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: A 318 SER cc_start: 0.7863 (m) cc_final: 0.7598 (t) REVERT: A 349 TYR cc_start: 0.8197 (m-80) cc_final: 0.7869 (m-80) REVERT: A 381 GLN cc_start: 0.6749 (mp10) cc_final: 0.5718 (mt0) REVERT: A 429 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6800 (tp) REVERT: A 447 MET cc_start: 0.7486 (ptm) cc_final: 0.7253 (ptp) REVERT: A 528 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7181 (p) REVERT: B 55 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 214 GLN cc_start: 0.7418 (mp10) cc_final: 0.6758 (mp10) REVERT: B 315 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 318 SER cc_start: 0.8048 (m) cc_final: 0.7776 (t) REVERT: B 349 TYR cc_start: 0.8171 (m-80) cc_final: 0.7868 (m-80) REVERT: B 372 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6839 (mt) REVERT: B 381 GLN cc_start: 0.6698 (mp10) cc_final: 0.5756 (mt0) REVERT: B 447 MET cc_start: 0.7420 (mtp) cc_final: 0.7086 (ttm) REVERT: B 528 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7064 (p) REVERT: C 46 ASP cc_start: 0.7860 (m-30) cc_final: 0.7428 (m-30) REVERT: C 62 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7589 (mttt) REVERT: C 99 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.5774 (mpp) REVERT: C 214 GLN cc_start: 0.7622 (mp10) cc_final: 0.7253 (mp10) REVERT: C 215 MET cc_start: 0.8398 (mmm) cc_final: 0.8079 (tpp) REVERT: C 294 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 315 GLU cc_start: 0.7670 (mp0) cc_final: 0.7199 (mp0) REVERT: C 318 SER cc_start: 0.7862 (m) cc_final: 0.7579 (t) REVERT: C 429 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6663 (tp) REVERT: C 447 MET cc_start: 0.7627 (ptm) cc_final: 0.7296 (ptp) REVERT: C 497 MET cc_start: 0.7402 (ttt) cc_final: 0.7031 (ttt) REVERT: C 501 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (mp) REVERT: C 528 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7127 (p) REVERT: D 55 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 214 GLN cc_start: 0.7395 (mp10) cc_final: 0.6733 (mp10) REVERT: D 315 GLU cc_start: 0.7849 (mp0) cc_final: 0.7269 (mp0) REVERT: D 318 SER cc_start: 0.7883 (m) cc_final: 0.7595 (t) REVERT: D 349 TYR cc_start: 0.8170 (m-80) cc_final: 0.7853 (m-80) REVERT: D 429 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6682 (tp) REVERT: D 447 MET cc_start: 0.7474 (mtp) cc_final: 0.7080 (ttm) REVERT: D 528 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7086 (p) outliers start: 45 outliers final: 23 residues processed: 300 average time/residue: 0.5636 time to fit residues: 191.8483 Evaluate side-chains 295 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 380 HIS ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 370 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 380 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116133 restraints weight = 23582.395| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.30 r_work: 0.3281 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19860 Z= 0.143 Angle : 0.618 12.618 26964 Z= 0.306 Chirality : 0.042 0.266 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.372 27.717 2644 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.00 % Allowed : 20.52 % Favored : 77.48 % 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: 0.51 (0.18), residues: 2408 helix: 1.24 (0.14), residues: 1484 sheet: -1.89 (0.44), residues: 104 loop : -0.97 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 414 TYR 0.018 0.001 TYR C 328 PHE 0.010 0.001 PHE A 537 TRP 0.011 0.001 TRP A 286 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00336 (19860) covalent geometry : angle 0.61844 (26964) hydrogen bonds : bond 0.03843 ( 1060) hydrogen bonds : angle 4.11101 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6997.09 seconds wall clock time: 119 minutes 50.23 seconds (7190.23 seconds total)