Starting phenix.real_space_refine on Mon Jun 16 21:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6j_25716/06_2025/7t6j_25716.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.038 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 51 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.35, per 1000 atoms: 0.58 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 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: 4.58 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 128 helices and 8 sheets defined 66.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 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 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.871A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.644A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.616A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.345A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.518A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.539A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.050A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.782A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.811A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.607A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.948A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.890A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.536A 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 removed outlier: 3.896A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.604A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.565A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.114A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.567A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.696A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.531A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.342A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.531A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.520A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.039A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.770A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.811A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.614A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.971A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.883A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.536A 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 removed outlier: 3.959A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.884A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 536 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.523A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.067A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.560A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.863A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.642A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.517A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 193 through 197 removed outlier: 4.331A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 210 through 222 removed outlier: 4.512A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.517A pdb=" N GLY C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.051A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.783A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.797A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.592A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 402 removed outlier: 3.962A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.891A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.538A 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 removed outlier: 3.968A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.597A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 536 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 605 removed outlier: 4.084A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.565A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.695A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.538A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.343A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 222 removed outlier: 4.528A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.511A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.046A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.771A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.809A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.595A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 402 removed outlier: 3.952A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.884A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.537A 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 removed outlier: 3.934A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.602A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.887A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.603A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 605 removed outlier: 4.104A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.810A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (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 268 removed outlier: 6.814A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (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 268 removed outlier: 6.813A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (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 268 removed outlier: 6.814A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1061 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 5.45 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: 6145 1.34 - 1.46: 4426 1.46 - 1.58: 9061 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" SD MET A 554 " pdb=" CE MET A 554 " ideal model delta sigma weight residual 1.791 1.728 0.063 2.50e-02 1.60e+03 6.44e+00 bond pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.31e+00 bond pdb=" C ILE D 404 " pdb=" N PRO D 405 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.15e+00 bond pdb=" C ILE B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 6.03e+00 bond pdb=" C ILE C 404 " pdb=" N PRO C 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 5.97e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 26539 3.69 - 7.38: 370 7.38 - 11.07: 40 11.07 - 14.75: 7 14.75 - 18.44: 8 Bond angle restraints: 26964 Sorted by residual: angle pdb=" CA LEU A 536 " pdb=" CB LEU A 536 " pdb=" CG LEU A 536 " ideal model delta sigma weight residual 116.30 134.74 -18.44 3.50e+00 8.16e-02 2.78e+01 angle pdb=" CA LEU C 536 " pdb=" CB LEU C 536 " pdb=" CG LEU C 536 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU D 536 " pdb=" CB LEU D 536 " pdb=" CG LEU D 536 " ideal model delta sigma weight residual 116.30 134.40 -18.10 3.50e+00 8.16e-02 2.67e+01 angle pdb=" CA LEU B 536 " pdb=" CB LEU B 536 " pdb=" CG LEU B 536 " ideal model delta sigma weight residual 116.30 134.26 -17.96 3.50e+00 8.16e-02 2.63e+01 angle pdb=" C GLU B 403 " pdb=" N ILE B 404 " pdb=" CA ILE B 404 " ideal model delta sigma weight residual 120.24 123.47 -3.23 6.30e-01 2.52e+00 2.63e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10523 18.00 - 35.99: 1041 35.99 - 53.99: 188 53.99 - 71.98: 44 71.98 - 89.98: 16 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ASP B 406 " pdb=" C ASP B 406 " pdb=" N ILE B 407 " pdb=" CA ILE B 407 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP C 406 " pdb=" C ASP C 406 " pdb=" N ILE C 407 " pdb=" CA ILE C 407 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASP D 406 " pdb=" C ASP D 406 " pdb=" N ILE D 407 " pdb=" CA ILE D 407 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2915 0.117 - 0.234: 140 0.234 - 0.350: 11 0.350 - 0.467: 2 0.467 - 0.584: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL A 585 " pdb=" CA VAL A 585 " pdb=" CG1 VAL A 585 " pdb=" CG2 VAL A 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CB VAL D 585 " pdb=" CA VAL D 585 " pdb=" CG1 VAL D 585 " pdb=" CG2 VAL D 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 487 " 0.018 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE A 487 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 487 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 487 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 487 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 574 " 0.020 2.00e-02 2.50e+03 1.83e-02 5.86e+00 pdb=" CG PHE B 574 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 574 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 574 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 574 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 574 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 311 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 312 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.035 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6276 2.85 - 3.36: 17954 3.36 - 3.88: 32373 3.88 - 4.39: 37671 4.39 - 4.90: 64067 Nonbonded interactions: 158341 Sorted by model distance: nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.340 3.040 nonbonded pdb=" O MET C 577 " pdb=" OG1 THR C 581 " model vdw 2.342 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.342 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.351 3.040 nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.361 3.040 ... (remaining 158336 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: 0.15 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: 7.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.900 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 0.065 19860 Z= 0.257 Angle : 1.093 18.443 26964 Z= 0.556 Chirality : 0.061 0.584 3072 Planarity : 0.008 0.060 3416 Dihedral : 14.919 89.976 7236 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.13), residues: 2408 helix: -2.38 (0.10), residues: 1420 sheet: -0.78 (0.48), residues: 92 loop : -1.75 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 268 HIS 0.005 0.001 HIS C 201 PHE 0.055 0.003 PHE A 487 TYR 0.017 0.002 TYR B 547 ARG 0.005 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.14193 ( 1061) hydrogen bonds : angle 6.88289 ( 3048) covalent geometry : bond 0.00524 (19860) covalent geometry : angle 1.09294 (26964) *********************** 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 340 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 2.183 Fit side-chains REVERT: A 177 GLU cc_start: 0.7814 (mp0) cc_final: 0.7501 (pm20) REVERT: A 255 MET cc_start: 0.8830 (tpp) cc_final: 0.8623 (tpp) REVERT: A 302 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7474 (ttm-80) REVERT: A 481 MET cc_start: 0.8743 (tpt) cc_final: 0.8306 (tpt) REVERT: B 55 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 177 GLU cc_start: 0.7800 (mp0) cc_final: 0.7535 (pm20) REVERT: B 302 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7467 (ttm-80) REVERT: B 440 MET cc_start: 0.7935 (ttp) cc_final: 0.7628 (ttp) REVERT: B 481 MET cc_start: 0.8731 (tpt) cc_final: 0.8273 (tpt) REVERT: C 177 GLU cc_start: 0.7822 (mp0) cc_final: 0.7514 (pm20) REVERT: C 302 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7479 (ttm-80) REVERT: D 177 GLU cc_start: 0.7801 (mp0) cc_final: 0.7532 (pm20) REVERT: D 302 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7470 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2887 time to fit residues: 154.2853 Evaluate side-chains 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 261 GLN A 513 GLN A 635 ASN B 208 ASN B 261 GLN B 513 GLN B 635 ASN C 197 ASN C 208 ASN C 214 GLN C 261 GLN C 513 GLN C 635 ASN D 208 ASN D 261 GLN D 513 GLN D 635 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.086733 restraints weight = 29284.823| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.78 r_work: 0.2907 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19860 Z= 0.160 Angle : 0.636 12.312 26964 Z= 0.315 Chirality : 0.042 0.215 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.731 22.408 2644 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.28 % Favored : 97.55 % Rotamer: Outliers : 0.72 % Allowed : 9.54 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2408 helix: -0.31 (0.13), residues: 1464 sheet: -0.73 (0.49), residues: 92 loop : -1.16 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 583 HIS 0.006 0.001 HIS D 426 PHE 0.019 0.001 PHE B 574 TYR 0.010 0.001 TYR A 555 ARG 0.002 0.000 ARG B 632 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1061) hydrogen bonds : angle 4.26879 ( 3048) covalent geometry : bond 0.00374 (19860) covalent geometry : angle 0.63575 (26964) *********************** 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 259 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 2.556 Fit side-chains REVERT: A 177 GLU cc_start: 0.8353 (mp0) cc_final: 0.7951 (pm20) REVERT: A 487 PHE cc_start: 0.8325 (m-10) cc_final: 0.8123 (m-10) REVERT: B 55 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 177 GLU cc_start: 0.8318 (mp0) cc_final: 0.7949 (pm20) REVERT: B 637 HIS cc_start: 0.7818 (p-80) cc_final: 0.7469 (p90) REVERT: C 177 GLU cc_start: 0.8329 (mp0) cc_final: 0.7928 (pm20) REVERT: C 487 PHE cc_start: 0.8178 (m-10) cc_final: 0.7976 (m-10) REVERT: C 637 HIS cc_start: 0.7845 (p-80) cc_final: 0.7381 (p90) REVERT: D 55 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 177 GLU cc_start: 0.8321 (mp0) cc_final: 0.7950 (pm20) REVERT: D 637 HIS cc_start: 0.7845 (p-80) cc_final: 0.7362 (p90) outliers start: 15 outliers final: 12 residues processed: 253 average time/residue: 0.2935 time to fit residues: 118.6843 Evaluate side-chains 230 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 197 ASN B 252 ASN B 310 GLN C 252 ASN C 310 GLN D 197 ASN D 252 ASN D 310 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.079987 restraints weight = 29345.005| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.78 r_work: 0.2753 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19860 Z= 0.259 Angle : 0.683 11.993 26964 Z= 0.341 Chirality : 0.046 0.234 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.774 22.262 2644 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.45 % Favored : 97.38 % Rotamer: Outliers : 2.05 % Allowed : 11.64 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2408 helix: 0.27 (0.13), residues: 1472 sheet: -0.71 (0.49), residues: 92 loop : -1.05 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 321 HIS 0.006 0.001 HIS B 426 PHE 0.012 0.002 PHE B 574 TYR 0.010 0.002 TYR A 89 ARG 0.004 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 1061) hydrogen bonds : angle 4.30494 ( 3048) covalent geometry : bond 0.00634 (19860) covalent geometry : angle 0.68346 (26964) *********************** 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 270 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 3.687 Fit side-chains REVERT: A 112 CYS cc_start: 0.7479 (m) cc_final: 0.7054 (m) REVERT: A 177 GLU cc_start: 0.8296 (mp0) cc_final: 0.7909 (pm20) REVERT: B 177 GLU cc_start: 0.8260 (mp0) cc_final: 0.7892 (pm20) REVERT: B 540 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8797 (mt) REVERT: B 554 MET cc_start: 0.8791 (tpt) cc_final: 0.8549 (tpt) REVERT: C 112 CYS cc_start: 0.7475 (m) cc_final: 0.7048 (m) REVERT: C 177 GLU cc_start: 0.8334 (mp0) cc_final: 0.7936 (pm20) REVERT: C 487 PHE cc_start: 0.8537 (m-10) cc_final: 0.8333 (m-10) REVERT: D 177 GLU cc_start: 0.8309 (mp0) cc_final: 0.7936 (pm20) outliers start: 43 outliers final: 26 residues processed: 261 average time/residue: 0.3080 time to fit residues: 130.4736 Evaluate side-chains 241 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 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 252 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.093867 restraints weight = 28269.557| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.61 r_work: 0.2925 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19860 Z= 0.116 Angle : 0.554 9.522 26964 Z= 0.274 Chirality : 0.040 0.203 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.354 19.575 2644 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.37 % Favored : 97.47 % Rotamer: Outliers : 1.10 % Allowed : 14.17 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2408 helix: 0.81 (0.14), residues: 1460 sheet: -0.94 (0.45), residues: 92 loop : -0.74 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS D 426 PHE 0.018 0.001 PHE C 574 TYR 0.009 0.001 TYR B 555 ARG 0.002 0.000 ARG B 632 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 1061) hydrogen bonds : angle 3.93774 ( 3048) covalent geometry : bond 0.00259 (19860) covalent geometry : angle 0.55366 (26964) *********************** 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 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 2.941 Fit side-chains REVERT: A 177 GLU cc_start: 0.8167 (mp0) cc_final: 0.7930 (pm20) REVERT: B 177 GLU cc_start: 0.8144 (mp0) cc_final: 0.7932 (pm20) REVERT: C 177 GLU cc_start: 0.8227 (mp0) cc_final: 0.7972 (pm20) REVERT: D 177 GLU cc_start: 0.8201 (mp0) cc_final: 0.7965 (pm20) outliers start: 23 outliers final: 12 residues processed: 250 average time/residue: 0.3119 time to fit residues: 124.3512 Evaluate side-chains 224 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 596 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094834 restraints weight = 28327.093| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.58 r_work: 0.2935 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19860 Z= 0.126 Angle : 0.555 8.824 26964 Z= 0.273 Chirality : 0.040 0.194 3072 Planarity : 0.004 0.036 3416 Dihedral : 4.278 19.140 2644 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 15.74 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2408 helix: 1.13 (0.14), residues: 1460 sheet: -0.91 (0.44), residues: 92 loop : -0.66 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 593 HIS 0.003 0.001 HIS D 426 PHE 0.021 0.001 PHE C 574 TYR 0.009 0.001 TYR B 555 ARG 0.002 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1061) hydrogen bonds : angle 3.82833 ( 3048) covalent geometry : bond 0.00294 (19860) covalent geometry : angle 0.55466 (26964) *********************** 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 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 2.096 Fit side-chains REVERT: A 177 GLU cc_start: 0.8210 (mp0) cc_final: 0.7939 (pm20) REVERT: A 522 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: B 177 GLU cc_start: 0.8186 (mp0) cc_final: 0.7936 (pm20) REVERT: B 481 MET cc_start: 0.9304 (tpp) cc_final: 0.9077 (tpt) REVERT: B 522 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: B 554 MET cc_start: 0.8774 (tpt) cc_final: 0.8548 (tpt) REVERT: C 177 GLU cc_start: 0.8246 (mp0) cc_final: 0.7990 (pm20) REVERT: C 522 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: D 177 GLU cc_start: 0.8231 (mp0) cc_final: 0.7966 (pm20) REVERT: D 522 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8531 (mp0) outliers start: 27 outliers final: 16 residues processed: 241 average time/residue: 0.2836 time to fit residues: 108.7931 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092031 restraints weight = 28468.259| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.61 r_work: 0.2910 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19860 Z= 0.131 Angle : 0.548 8.334 26964 Z= 0.271 Chirality : 0.040 0.195 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.206 18.854 2644 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.38 % Allowed : 16.03 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2408 helix: 1.32 (0.14), residues: 1468 sheet: -0.90 (0.44), residues: 92 loop : -0.64 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 593 HIS 0.003 0.001 HIS C 426 PHE 0.011 0.001 PHE C 574 TYR 0.010 0.001 TYR B 555 ARG 0.002 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 1061) hydrogen bonds : angle 3.78182 ( 3048) covalent geometry : bond 0.00308 (19860) covalent geometry : angle 0.54795 (26964) *********************** 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 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 2.171 Fit side-chains REVERT: A 177 GLU cc_start: 0.8230 (mp0) cc_final: 0.7976 (pm20) REVERT: B 177 GLU cc_start: 0.8190 (mp0) cc_final: 0.7953 (pm20) REVERT: B 481 MET cc_start: 0.9301 (tpp) cc_final: 0.9034 (tpt) REVERT: B 522 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: C 177 GLU cc_start: 0.8217 (mp0) cc_final: 0.7996 (pm20) REVERT: D 177 GLU cc_start: 0.8251 (mp0) cc_final: 0.7998 (pm20) REVERT: D 522 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8509 (mp0) outliers start: 29 outliers final: 17 residues processed: 250 average time/residue: 0.2822 time to fit residues: 112.8313 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095226 restraints weight = 28119.958| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.57 r_work: 0.2931 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.118 Angle : 0.555 11.815 26964 Z= 0.270 Chirality : 0.039 0.185 3072 Planarity : 0.004 0.036 3416 Dihedral : 4.153 19.841 2644 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.38 % Allowed : 15.89 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2408 helix: 1.46 (0.14), residues: 1468 sheet: -0.77 (0.46), residues: 92 loop : -0.55 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.002 0.000 HIS D 426 PHE 0.025 0.001 PHE C 574 TYR 0.018 0.001 TYR D 547 ARG 0.002 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1061) hydrogen bonds : angle 3.73240 ( 3048) covalent geometry : bond 0.00274 (19860) covalent geometry : angle 0.55477 (26964) *********************** 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 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 2.395 Fit side-chains REVERT: A 177 GLU cc_start: 0.8215 (mp0) cc_final: 0.7945 (pm20) REVERT: B 177 GLU cc_start: 0.8187 (mp0) cc_final: 0.7928 (pm20) REVERT: B 481 MET cc_start: 0.9296 (tpp) cc_final: 0.9043 (tpt) REVERT: B 522 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: C 177 GLU cc_start: 0.8230 (mp0) cc_final: 0.7974 (pm20) REVERT: D 177 GLU cc_start: 0.8226 (mp0) cc_final: 0.7953 (pm20) REVERT: D 522 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (mp0) outliers start: 29 outliers final: 18 residues processed: 249 average time/residue: 0.2851 time to fit residues: 114.8937 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.0020 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.090023 restraints weight = 29046.414| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.70 r_work: 0.2933 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.099 Angle : 0.534 10.735 26964 Z= 0.261 Chirality : 0.038 0.177 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.031 17.893 2644 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.15 % Allowed : 16.56 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2408 helix: 1.62 (0.14), residues: 1476 sheet: -0.63 (0.47), residues: 92 loop : -0.50 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.002 0.000 HIS D 426 PHE 0.019 0.001 PHE A 574 TYR 0.016 0.001 TYR A 555 ARG 0.001 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1061) hydrogen bonds : angle 3.68400 ( 3048) covalent geometry : bond 0.00214 (19860) covalent geometry : angle 0.53417 (26964) *********************** 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 265 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 2.239 Fit side-chains REVERT: A 177 GLU cc_start: 0.8226 (mp0) cc_final: 0.7970 (pm20) REVERT: A 596 GLN cc_start: 0.8356 (pt0) cc_final: 0.8134 (pt0) REVERT: B 177 GLU cc_start: 0.8179 (mp0) cc_final: 0.7941 (pm20) REVERT: B 481 MET cc_start: 0.9275 (tpp) cc_final: 0.9072 (tpt) REVERT: C 177 GLU cc_start: 0.8251 (mp0) cc_final: 0.8005 (pm20) REVERT: D 177 GLU cc_start: 0.8261 (mp0) cc_final: 0.7997 (pm20) REVERT: D 522 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8525 (mp0) outliers start: 24 outliers final: 17 residues processed: 258 average time/residue: 0.2742 time to fit residues: 114.2358 Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 0.9990 chunk 140 optimal weight: 0.0980 chunk 154 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.089011 restraints weight = 29053.515| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.72 r_work: 0.2909 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19860 Z= 0.107 Angle : 0.545 10.689 26964 Z= 0.266 Chirality : 0.038 0.177 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.988 18.271 2644 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.86 % Allowed : 16.98 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2408 helix: 1.74 (0.14), residues: 1472 sheet: -0.70 (0.47), residues: 92 loop : -0.46 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.002 0.000 HIS D 426 PHE 0.013 0.001 PHE C 574 TYR 0.018 0.001 TYR C 555 ARG 0.002 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1061) hydrogen bonds : angle 3.69612 ( 3048) covalent geometry : bond 0.00247 (19860) covalent geometry : angle 0.54506 (26964) *********************** 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 248 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 2.099 Fit side-chains REVERT: A 177 GLU cc_start: 0.8244 (mp0) cc_final: 0.7981 (pm20) REVERT: A 596 GLN cc_start: 0.8401 (pt0) cc_final: 0.8145 (pt0) REVERT: B 177 GLU cc_start: 0.8199 (mp0) cc_final: 0.7933 (pm20) REVERT: B 481 MET cc_start: 0.9319 (tpp) cc_final: 0.9109 (tpt) REVERT: B 501 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8742 (mp) REVERT: C 177 GLU cc_start: 0.8253 (mp0) cc_final: 0.7985 (pm20) REVERT: C 487 PHE cc_start: 0.7969 (m-10) cc_final: 0.7763 (m-10) REVERT: D 177 GLU cc_start: 0.8269 (mp0) cc_final: 0.7978 (pm20) REVERT: D 522 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8550 (mp0) outliers start: 18 outliers final: 14 residues processed: 244 average time/residue: 0.2794 time to fit residues: 110.4002 Evaluate side-chains 242 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.086377 restraints weight = 29172.793| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.72 r_work: 0.2877 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19860 Z= 0.130 Angle : 0.568 11.172 26964 Z= 0.278 Chirality : 0.039 0.185 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.045 19.601 2644 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.95 % Allowed : 16.98 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2408 helix: 1.71 (0.14), residues: 1476 sheet: -0.74 (0.47), residues: 92 loop : -0.47 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.002 0.001 HIS C 426 PHE 0.029 0.001 PHE C 574 TYR 0.016 0.001 TYR C 547 ARG 0.003 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 1061) hydrogen bonds : angle 3.73156 ( 3048) covalent geometry : bond 0.00312 (19860) covalent geometry : angle 0.56793 (26964) ********************** 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 245 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 2.116 Fit side-chains REVERT: A 177 GLU cc_start: 0.8243 (mp0) cc_final: 0.7979 (pm20) REVERT: B 177 GLU cc_start: 0.8234 (mp0) cc_final: 0.7959 (pm20) REVERT: B 481 MET cc_start: 0.9354 (tpp) cc_final: 0.9154 (tpt) REVERT: B 487 PHE cc_start: 0.8142 (m-10) cc_final: 0.7942 (m-10) REVERT: B 501 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 522 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: C 177 GLU cc_start: 0.8267 (mp0) cc_final: 0.7994 (pm20) REVERT: C 487 PHE cc_start: 0.8093 (m-10) cc_final: 0.7882 (m-10) REVERT: D 177 GLU cc_start: 0.8312 (mp0) cc_final: 0.8017 (pm20) REVERT: D 522 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: D 554 MET cc_start: 0.8938 (mmm) cc_final: 0.8353 (tpt) outliers start: 20 outliers final: 14 residues processed: 240 average time/residue: 0.3105 time to fit residues: 119.3350 Evaluate side-chains 237 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 18 optimal weight: 3.9990 chunk 211 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090298 restraints weight = 29089.438| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.72 r_work: 0.2931 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19860 Z= 0.102 Angle : 0.541 10.282 26964 Z= 0.265 Chirality : 0.038 0.174 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.941 17.907 2644 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.76 % Allowed : 17.27 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2408 helix: 1.83 (0.14), residues: 1468 sheet: -0.78 (0.46), residues: 92 loop : -0.45 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.002 0.000 HIS C 201 PHE 0.027 0.001 PHE C 574 TYR 0.016 0.001 TYR A 555 ARG 0.002 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 1061) hydrogen bonds : angle 3.67009 ( 3048) covalent geometry : bond 0.00228 (19860) covalent geometry : angle 0.54051 (26964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10801.12 seconds wall clock time: 191 minutes 19.22 seconds (11479.22 seconds total)