Starting phenix.real_space_refine on Thu Mar 5 04:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6j_25716/03_2026/7t6j_25716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6j_25716/03_2026/7t6j_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_25716/03_2026/7t6j_25716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6j_25716/03_2026/7t6j_25716.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6j_25716/03_2026/7t6j_25716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6j_25716/03_2026/7t6j_25716.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 4.41, per 1000 atoms: 0.23 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: 1.61 Conformation dependent library (CDL) restraints added in 825.2 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 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: 0.53 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: 3.14 Time building geometry restraints manager: 2.15 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: 0.01 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: 1.550 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (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 ARG 0.005 0.001 ARG A 385 TYR 0.017 0.002 TYR B 547 PHE 0.055 0.003 PHE A 487 TRP 0.014 0.002 TRP B 268 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00524 (19860) covalent geometry : angle 1.09294 (26964) hydrogen bonds : bond 0.14193 ( 1061) hydrogen bonds : angle 6.88289 ( 3048) *********************** 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 : 0.749 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: 0.1308 time to fit residues: 70.9528 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 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 261 GLN A 513 GLN A 635 ASN B 208 ASN B 261 GLN B 513 GLN B 635 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100147 restraints weight = 28265.142| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.62 r_work: 0.3009 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19860 Z= 0.128 Angle : 0.604 11.459 26964 Z= 0.299 Chirality : 0.041 0.205 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.668 21.819 2644 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.03 % Favored : 97.80 % Rotamer: Outliers : 0.57 % Allowed : 9.40 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2408 helix: -0.24 (0.13), residues: 1460 sheet: -0.74 (0.48), residues: 92 loop : -1.15 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.011 0.001 TYR A 555 PHE 0.020 0.001 PHE B 574 TRP 0.006 0.001 TRP B 462 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00290 (19860) covalent geometry : angle 0.60435 (26964) hydrogen bonds : bond 0.03901 ( 1061) hydrogen bonds : angle 4.20566 ( 3048) *********************** 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 266 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 254 time to evaluate : 0.456 Fit side-chains REVERT: A 177 GLU cc_start: 0.8285 (mp0) cc_final: 0.7984 (pm20) REVERT: B 55 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 177 GLU cc_start: 0.8251 (mp0) cc_final: 0.7961 (pm20) REVERT: B 554 MET cc_start: 0.8254 (tpt) cc_final: 0.8014 (tpt) REVERT: B 637 HIS cc_start: 0.7788 (p-80) cc_final: 0.7530 (p90) REVERT: C 177 GLU cc_start: 0.8252 (mp0) cc_final: 0.7954 (pm20) REVERT: C 487 PHE cc_start: 0.7918 (m-10) cc_final: 0.7717 (m-10) REVERT: C 637 HIS cc_start: 0.7801 (p-80) cc_final: 0.7475 (p90) REVERT: D 55 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7842 (mm-30) REVERT: D 177 GLU cc_start: 0.8258 (mp0) cc_final: 0.7965 (pm20) outliers start: 12 outliers final: 8 residues processed: 263 average time/residue: 0.1153 time to fit residues: 49.0559 Evaluate side-chains 230 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 452 VAL Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 394 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 217 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN B 252 ASN B 310 GLN C 197 ASN C 252 ASN C 310 GLN 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 = 0.3244 r_free = 0.3244 target = 0.109512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.086284 restraints weight = 29426.367| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.82 r_work: 0.2874 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.139 Angle : 0.580 10.232 26964 Z= 0.286 Chirality : 0.041 0.206 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.428 20.264 2644 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 1.05 % Allowed : 11.78 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2408 helix: 0.54 (0.13), residues: 1468 sheet: -0.70 (0.46), residues: 92 loop : -0.90 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.009 0.001 TYR D 555 PHE 0.021 0.001 PHE C 574 TRP 0.005 0.001 TRP A 593 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00326 (19860) covalent geometry : angle 0.57961 (26964) hydrogen bonds : bond 0.03779 ( 1061) hydrogen bonds : angle 4.01348 ( 3048) *********************** 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 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.631 Fit side-chains REVERT: A 112 CYS cc_start: 0.7136 (m) cc_final: 0.6888 (m) REVERT: A 177 GLU cc_start: 0.8313 (mp0) cc_final: 0.7904 (pm20) REVERT: A 378 VAL cc_start: 0.8712 (m) cc_final: 0.8485 (t) REVERT: B 177 GLU cc_start: 0.8294 (mp0) cc_final: 0.7905 (pm20) REVERT: B 378 VAL cc_start: 0.8720 (m) cc_final: 0.8509 (t) REVERT: B 487 PHE cc_start: 0.8206 (m-10) cc_final: 0.7985 (m-10) REVERT: C 177 GLU cc_start: 0.8290 (mp0) cc_final: 0.7908 (pm20) REVERT: C 378 VAL cc_start: 0.8700 (m) cc_final: 0.8487 (t) REVERT: C 487 PHE cc_start: 0.8223 (m-10) cc_final: 0.7712 (m-10) REVERT: D 177 GLU cc_start: 0.8321 (mp0) cc_final: 0.7927 (pm20) REVERT: D 378 VAL cc_start: 0.8718 (m) cc_final: 0.8476 (t) REVERT: D 487 PHE cc_start: 0.8221 (m-10) cc_final: 0.7982 (m-10) outliers start: 22 outliers final: 9 residues processed: 271 average time/residue: 0.1175 time to fit residues: 51.8662 Evaluate side-chains 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.120989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100140 restraints weight = 28063.928| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.54 r_work: 0.3004 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19860 Z= 0.105 Angle : 0.533 8.898 26964 Z= 0.264 Chirality : 0.039 0.192 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.192 19.059 2644 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.67 % Allowed : 13.84 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2408 helix: 1.00 (0.14), residues: 1460 sheet: -0.87 (0.44), residues: 92 loop : -0.66 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.010 0.001 TYR B 555 PHE 0.027 0.001 PHE C 574 TRP 0.006 0.001 TRP A 593 HIS 0.002 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00231 (19860) covalent geometry : angle 0.53266 (26964) hydrogen bonds : bond 0.03407 ( 1061) hydrogen bonds : angle 3.81145 ( 3048) *********************** 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 264 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.674 Fit side-chains REVERT: A 177 GLU cc_start: 0.8189 (mp0) cc_final: 0.7933 (pm20) REVERT: A 378 VAL cc_start: 0.8640 (m) cc_final: 0.8430 (t) REVERT: A 637 HIS cc_start: 0.7906 (p-80) cc_final: 0.7640 (p90) REVERT: B 177 GLU cc_start: 0.8163 (mp0) cc_final: 0.7932 (pm20) REVERT: B 378 VAL cc_start: 0.8654 (m) cc_final: 0.8443 (t) REVERT: C 177 GLU cc_start: 0.8211 (mp0) cc_final: 0.7944 (pm20) REVERT: C 378 VAL cc_start: 0.8646 (m) cc_final: 0.8443 (t) REVERT: D 177 GLU cc_start: 0.8212 (mp0) cc_final: 0.7958 (pm20) REVERT: D 378 VAL cc_start: 0.8618 (m) cc_final: 0.8400 (t) outliers start: 14 outliers final: 9 residues processed: 259 average time/residue: 0.1164 time to fit residues: 49.0750 Evaluate side-chains 239 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU 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 29 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 197 ASN D 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097512 restraints weight = 28086.561| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.59 r_work: 0.2961 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2246 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= 0.110 Angle : 0.527 8.472 26964 Z= 0.262 Chirality : 0.039 0.189 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.119 19.181 2644 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.29 % Allowed : 14.46 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2408 helix: 1.30 (0.14), residues: 1460 sheet: -0.92 (0.43), residues: 92 loop : -0.64 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.010 0.001 TYR B 555 PHE 0.007 0.001 PHE C 574 TRP 0.005 0.001 TRP B 593 HIS 0.002 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00251 (19860) covalent geometry : angle 0.52709 (26964) hydrogen bonds : bond 0.03372 ( 1061) hydrogen bonds : angle 3.77242 ( 3048) *********************** 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 275 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.617 Fit side-chains REVERT: A 177 GLU cc_start: 0.8229 (mp0) cc_final: 0.7910 (pm20) REVERT: A 302 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.7810 (ttm-80) REVERT: B 177 GLU cc_start: 0.8211 (mp0) cc_final: 0.7912 (pm20) REVERT: B 302 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.7774 (ttm-80) REVERT: C 177 GLU cc_start: 0.8230 (mp0) cc_final: 0.7910 (pm20) REVERT: C 302 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.7812 (ttm-80) REVERT: D 177 GLU cc_start: 0.8219 (mp0) cc_final: 0.7911 (pm20) REVERT: D 378 VAL cc_start: 0.8600 (m) cc_final: 0.8397 (t) outliers start: 27 outliers final: 12 residues processed: 271 average time/residue: 0.1261 time to fit residues: 55.0803 Evaluate side-chains 251 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 238 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 261 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099251 restraints weight = 28046.977| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.53 r_work: 0.2870 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.111 Angle : 0.537 11.250 26964 Z= 0.265 Chirality : 0.039 0.188 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.062 18.730 2644 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.76 % Allowed : 15.36 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2408 helix: 1.40 (0.14), residues: 1468 sheet: -0.77 (0.44), residues: 92 loop : -0.54 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.010 0.001 TYR B 555 PHE 0.025 0.001 PHE B 574 TRP 0.005 0.001 TRP C 593 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00254 (19860) covalent geometry : angle 0.53733 (26964) hydrogen bonds : bond 0.03367 ( 1061) hydrogen bonds : angle 3.78904 ( 3048) *********************** 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 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.783 Fit side-chains REVERT: A 177 GLU cc_start: 0.8248 (mp0) cc_final: 0.7820 (pm20) REVERT: A 302 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.7718 (ttm-80) REVERT: B 177 GLU cc_start: 0.8241 (mp0) cc_final: 0.7828 (pm20) REVERT: B 302 ARG cc_start: 0.8412 (mtp-110) cc_final: 0.7689 (ttm-80) REVERT: C 177 GLU cc_start: 0.8238 (mp0) cc_final: 0.7806 (pm20) REVERT: D 177 GLU cc_start: 0.8248 (mp0) cc_final: 0.7821 (pm20) outliers start: 16 outliers final: 13 residues processed: 250 average time/residue: 0.1264 time to fit residues: 50.8341 Evaluate side-chains 246 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL 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 213 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 192 optimal weight: 0.0070 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- 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 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 = 0.3349 r_free = 0.3349 target = 0.117042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095863 restraints weight = 28100.472| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.54 r_work: 0.2815 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2554 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= 0.146 Angle : 0.573 11.337 26964 Z= 0.282 Chirality : 0.040 0.194 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.157 20.174 2644 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.95 % Allowed : 16.03 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2408 helix: 1.50 (0.14), residues: 1444 sheet: -0.90 (0.43), residues: 92 loop : -0.55 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 632 TYR 0.010 0.001 TYR B 555 PHE 0.024 0.001 PHE C 574 TRP 0.005 0.001 TRP A 583 HIS 0.003 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00353 (19860) covalent geometry : angle 0.57306 (26964) hydrogen bonds : bond 0.03670 ( 1061) hydrogen bonds : angle 3.87592 ( 3048) *********************** 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 256 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.555 Fit side-chains REVERT: A 177 GLU cc_start: 0.8283 (mp0) cc_final: 0.7869 (pm20) REVERT: A 302 ARG cc_start: 0.8501 (mtp-110) cc_final: 0.7813 (ttm-80) REVERT: A 522 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: A 554 MET cc_start: 0.8941 (mmm) cc_final: 0.8687 (tpt) REVERT: B 177 GLU cc_start: 0.8257 (mp0) cc_final: 0.7845 (pm20) REVERT: B 302 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.7789 (ttm-80) REVERT: B 554 MET cc_start: 0.8516 (tpt) cc_final: 0.8277 (tpt) REVERT: C 177 GLU cc_start: 0.8243 (mp0) cc_final: 0.7821 (pm20) REVERT: D 177 GLU cc_start: 0.8287 (mp0) cc_final: 0.7863 (pm20) outliers start: 20 outliers final: 14 residues processed: 251 average time/residue: 0.1155 time to fit residues: 46.9173 Evaluate side-chains 243 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU 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 B residue 592 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3378 r_free = 0.3378 target = 0.118827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097349 restraints weight = 28185.187| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.58 r_work: 0.2858 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19860 Z= 0.107 Angle : 0.538 10.370 26964 Z= 0.266 Chirality : 0.039 0.182 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.028 19.009 2644 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.86 % Allowed : 16.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2408 helix: 1.65 (0.14), residues: 1444 sheet: -0.67 (0.46), residues: 92 loop : -0.45 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 632 TYR 0.010 0.001 TYR B 555 PHE 0.032 0.001 PHE B 574 TRP 0.006 0.001 TRP C 593 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00244 (19860) covalent geometry : angle 0.53826 (26964) hydrogen bonds : bond 0.03328 ( 1061) hydrogen bonds : angle 3.78666 ( 3048) *********************** 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 241 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.633 Fit side-chains REVERT: A 177 GLU cc_start: 0.8282 (mp0) cc_final: 0.7854 (pm20) REVERT: A 302 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.7767 (ttm-80) REVERT: A 522 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: B 177 GLU cc_start: 0.8261 (mp0) cc_final: 0.7851 (pm20) REVERT: B 302 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.7726 (ttm-80) REVERT: B 554 MET cc_start: 0.8421 (tpt) cc_final: 0.8193 (tpt) REVERT: C 177 GLU cc_start: 0.8270 (mp0) cc_final: 0.7831 (pm20) REVERT: C 302 ARG cc_start: 0.8489 (mtp-110) cc_final: 0.7780 (ttm-80) REVERT: C 522 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: D 177 GLU cc_start: 0.8264 (mp0) cc_final: 0.7846 (pm20) REVERT: D 522 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (mp0) outliers start: 18 outliers final: 11 residues processed: 234 average time/residue: 0.1255 time to fit residues: 46.6695 Evaluate side-chains 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU 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 232 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 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 = 0.3210 r_free = 0.3210 target = 0.106902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.083819 restraints weight = 29128.169| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.72 r_work: 0.2811 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19860 Z= 0.194 Angle : 0.620 11.809 26964 Z= 0.306 Chirality : 0.042 0.203 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.303 21.781 2644 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.05 % Allowed : 16.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2408 helix: 1.53 (0.14), residues: 1440 sheet: -0.94 (0.45), residues: 92 loop : -0.47 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 589 TYR 0.011 0.001 TYR B 555 PHE 0.031 0.002 PHE B 574 TRP 0.006 0.001 TRP A 583 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00474 (19860) covalent geometry : angle 0.61986 (26964) hydrogen bonds : bond 0.04048 ( 1061) hydrogen bonds : angle 3.97562 ( 3048) *********************** 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 240 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.659 Fit side-chains REVERT: A 177 GLU cc_start: 0.8296 (mp0) cc_final: 0.8039 (pm20) REVERT: A 302 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.7935 (ttm-80) REVERT: A 487 PHE cc_start: 0.8246 (m-10) cc_final: 0.8038 (m-10) REVERT: A 522 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: B 177 GLU cc_start: 0.8264 (mp0) cc_final: 0.8020 (pm20) REVERT: B 302 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.7896 (ttm-80) REVERT: B 522 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: C 177 GLU cc_start: 0.8261 (mp0) cc_final: 0.8006 (pm20) REVERT: C 302 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.7946 (ttm-80) REVERT: C 522 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: D 177 GLU cc_start: 0.8285 (mp0) cc_final: 0.8044 (pm20) REVERT: D 487 PHE cc_start: 0.8246 (m-10) cc_final: 0.8040 (m-10) REVERT: D 522 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8611 (mp0) outliers start: 22 outliers final: 14 residues processed: 236 average time/residue: 0.1274 time to fit residues: 47.7740 Evaluate side-chains 234 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS 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 253 THR 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 213 CYS Chi-restraints excluded: chain C residue 253 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 253 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 165 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 123 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 261 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097514 restraints weight = 28117.139| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.47 r_work: 0.2905 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19860 Z= 0.109 Angle : 0.554 10.243 26964 Z= 0.273 Chirality : 0.039 0.184 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.096 19.388 2644 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.67 % Allowed : 17.08 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2408 helix: 1.69 (0.14), residues: 1448 sheet: -0.75 (0.47), residues: 92 loop : -0.47 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 632 TYR 0.009 0.001 TYR A 555 PHE 0.029 0.001 PHE B 574 TRP 0.006 0.001 TRP B 593 HIS 0.003 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00247 (19860) covalent geometry : angle 0.55428 (26964) hydrogen bonds : bond 0.03409 ( 1061) hydrogen bonds : angle 3.83252 ( 3048) ********************** 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 237 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.765 Fit side-chains REVERT: A 177 GLU cc_start: 0.8174 (mp0) cc_final: 0.7945 (pm20) REVERT: A 302 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.7941 (ttm-80) REVERT: A 522 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: B 177 GLU cc_start: 0.8171 (mp0) cc_final: 0.7956 (pm20) REVERT: B 302 ARG cc_start: 0.8434 (mtp-110) cc_final: 0.7880 (ttm-80) REVERT: C 177 GLU cc_start: 0.8173 (mp0) cc_final: 0.7929 (pm20) REVERT: D 177 GLU cc_start: 0.8188 (mp0) cc_final: 0.7964 (pm20) REVERT: D 290 LEU cc_start: 0.7440 (pt) cc_final: 0.6515 (mt) REVERT: D 522 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8526 (mp0) outliers start: 14 outliers final: 10 residues processed: 234 average time/residue: 0.1278 time to fit residues: 48.1535 Evaluate side-chains 225 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 522 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain D residue 253 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 16 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 185 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096697 restraints weight = 28168.154| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.57 r_work: 0.2931 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19860 Z= 0.112 Angle : 0.557 10.304 26964 Z= 0.273 Chirality : 0.039 0.178 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.054 19.673 2644 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.67 % Allowed : 17.22 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.18), residues: 2408 helix: 1.78 (0.14), residues: 1452 sheet: -0.74 (0.46), residues: 92 loop : -0.44 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.020 0.001 TYR C 555 PHE 0.026 0.001 PHE B 574 TRP 0.006 0.001 TRP B 593 HIS 0.002 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00261 (19860) covalent geometry : angle 0.55683 (26964) hydrogen bonds : bond 0.03396 ( 1061) hydrogen bonds : angle 3.80761 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.46 seconds wall clock time: 74 minutes 40.61 seconds (4480.61 seconds total)