Starting phenix.real_space_refine on Thu Mar 5 08:34:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8c_24893/03_2026/7s8c_24893.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 160 5.16 5 Cl 13 4.86 5 C 13472 2.51 5 N 3336 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 20562 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 230 Unusual residues: {' CA': 1, ' CL': 1, 'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 228 Unusual residues: {'ECL': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.73, per 1000 atoms: 0.23 Number of scatterers: 20562 At special positions: 0 Unit cell: (130.624, 130.624, 122.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 Cl 13 17.00 S 160 16.00 P 4 15.00 O 3576 8.00 N 3336 7.00 C 13472 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: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.557A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.552A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.580A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.557A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.555A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.513A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.581A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.538A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.718A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 removed outlier: 3.557A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.573A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.671A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.506A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.634A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.747A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.632A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.581A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 3.927A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.558A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.554A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.572A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.759A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.825A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.551A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.624A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.754A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.514A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.670A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.505A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.635A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.107A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.746A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.633A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.580A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.539A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.717A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 580 removed outlier: 4.014A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 3.928A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.740A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.741A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1025 hydrogen bonds defined for protein. 2919 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: 3.78 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3196 1.31 - 1.44: 5552 1.44 - 1.56: 12000 1.56 - 1.69: 8 1.69 - 1.81: 284 Bond restraints: 21040 Sorted by residual: bond pdb=" C29 POV C 707 " pdb="C210 POV C 707 " ideal model delta sigma weight residual 1.333 1.554 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C29 POV D 708 " pdb="C210 POV D 708 " ideal model delta sigma weight residual 1.333 1.554 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C29 POV B 707 " pdb="C210 POV B 707 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C29 POV A 707 " pdb="C210 POV A 707 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C21 POV A 707 " pdb=" O21 POV A 707 " ideal model delta sigma weight residual 1.330 1.415 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 21035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 27876 3.21 - 6.42: 508 6.42 - 9.63: 97 9.63 - 12.84: 15 12.84 - 16.05: 8 Bond angle restraints: 28504 Sorted by residual: angle pdb=" C28 POV B 707 " pdb=" C29 POV B 707 " pdb="C210 POV B 707 " ideal model delta sigma weight residual 127.79 111.74 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C ASN C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C ASN B 546 " pdb=" N TYR B 547 " pdb=" CA TYR B 547 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C ASN D 546 " pdb=" N TYR D 547 " pdb=" CA TYR D 547 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ASN A 546 " pdb=" N TYR A 547 " pdb=" CA TYR A 547 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.79e+01 ... (remaining 28499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.19: 12702 28.19 - 56.38: 436 56.38 - 84.57: 80 84.57 - 112.76: 6 112.76 - 140.95: 12 Dihedral angle restraints: 13236 sinusoidal: 6076 harmonic: 7160 Sorted by residual: dihedral pdb=" CA MET C 466 " pdb=" C MET C 466 " pdb=" N TYR C 467 " pdb=" CA TYR C 467 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET A 466 " pdb=" C MET A 466 " pdb=" N TYR A 467 " pdb=" CA TYR A 467 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET B 466 " pdb=" C MET B 466 " pdb=" N TYR B 467 " pdb=" CA TYR B 467 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 13233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2509 0.064 - 0.128: 568 0.128 - 0.192: 92 0.192 - 0.256: 15 0.256 - 0.319: 16 Chirality restraints: 3200 Sorted by residual: chirality pdb=" CG LEU D 308 " pdb=" CB LEU D 308 " pdb=" CD1 LEU D 308 " pdb=" CD2 LEU D 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU C 308 " pdb=" CB LEU C 308 " pdb=" CD1 LEU C 308 " pdb=" CD2 LEU C 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3197 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 708 " 0.222 2.00e-02 2.50e+03 2.21e-01 4.88e+02 pdb=" C29 POV D 708 " -0.225 2.00e-02 2.50e+03 pdb="C210 POV D 708 " -0.217 2.00e-02 2.50e+03 pdb="C211 POV D 708 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 707 " -0.210 2.00e-02 2.50e+03 2.11e-01 4.45e+02 pdb=" C29 POV B 707 " 0.207 2.00e-02 2.50e+03 pdb="C210 POV B 707 " 0.214 2.00e-02 2.50e+03 pdb="C211 POV B 707 " -0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 707 " -0.204 2.00e-02 2.50e+03 2.04e-01 4.18e+02 pdb=" C29 POV A 707 " 0.204 2.00e-02 2.50e+03 pdb="C210 POV A 707 " 0.204 2.00e-02 2.50e+03 pdb="C211 POV A 707 " -0.204 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3754 2.76 - 3.29: 18688 3.29 - 3.83: 34462 3.83 - 4.36: 43855 4.36 - 4.90: 72202 Nonbonded interactions: 172961 Sorted by model distance: nonbonded pdb=" O MET B 577 " pdb=" OG1 THR B 581 " model vdw 2.221 3.040 nonbonded pdb=" O MET D 577 " pdb=" OG1 THR D 581 " model vdw 2.222 3.040 nonbonded pdb=" O MET C 577 " pdb=" OG1 THR C 581 " model vdw 2.222 3.040 nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.222 3.040 nonbonded pdb=" O11 POV A 706 " pdb=" O21 POV A 706 " model vdw 2.342 2.432 ... (remaining 172956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'B' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'C' and (resid 27 through 638 or resid 703 through 704 or (resid 706 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ or resid 707)) selection = (chain 'D' and (resid 27 through 638 or resid 703 through 704 or resid 706 or (r \ esid 707 and (name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C29 or name O21 or name O22 or nam \ e C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)))) } 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=0.45 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: 1.110 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: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.500 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.221 21040 Z= 0.455 Angle : 1.187 16.050 28504 Z= 0.606 Chirality : 0.059 0.319 3200 Planarity : 0.011 0.221 3512 Dihedral : 14.480 140.949 8612 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.75 % Allowed : 3.77 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.12), residues: 2440 helix: -3.68 (0.08), residues: 1468 sheet: -1.73 (0.45), residues: 124 loop : -1.82 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG D 33 TYR 0.023 0.004 TYR C 216 PHE 0.027 0.004 PHE A 169 TRP 0.024 0.004 TRP C 629 HIS 0.016 0.003 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.01047 (21040) covalent geometry : angle 1.18657 (28504) hydrogen bonds : bond 0.27587 ( 1025) hydrogen bonds : angle 8.69956 ( 2919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 550 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7279 (tp40) cc_final: 0.6933 (tp-100) REVERT: A 41 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7980 (mp-120) REVERT: A 99 MET cc_start: 0.6109 (mtm) cc_final: 0.5812 (mtm) REVERT: A 178 ILE cc_start: 0.8167 (mt) cc_final: 0.7905 (mt) REVERT: B 31 GLN cc_start: 0.7278 (tp40) cc_final: 0.7009 (tp-100) REVERT: B 41 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7962 (mp-120) REVERT: B 99 MET cc_start: 0.6113 (mtm) cc_final: 0.5839 (mtm) REVERT: B 178 ILE cc_start: 0.8143 (mt) cc_final: 0.7855 (mt) REVERT: C 31 GLN cc_start: 0.7284 (tp40) cc_final: 0.6876 (tp-100) REVERT: C 41 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7983 (mp-120) REVERT: C 99 MET cc_start: 0.6062 (mtm) cc_final: 0.5770 (mtm) REVERT: C 178 ILE cc_start: 0.8135 (mt) cc_final: 0.7873 (mt) REVERT: C 591 GLU cc_start: 0.6990 (tt0) cc_final: 0.6783 (tt0) REVERT: D 31 GLN cc_start: 0.7298 (tp40) cc_final: 0.6897 (tp-100) REVERT: D 41 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7973 (mp-120) REVERT: D 99 MET cc_start: 0.6100 (mtm) cc_final: 0.5803 (mtm) REVERT: D 178 ILE cc_start: 0.8155 (mt) cc_final: 0.7888 (mt) REVERT: D 481 MET cc_start: 0.6427 (ttm) cc_final: 0.6136 (tpp) outliers start: 16 outliers final: 0 residues processed: 562 average time/residue: 0.6296 time to fit residues: 395.9883 Evaluate side-chains 398 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 122 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 369 GLN A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 74 GLN B 91 ASN B 122 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 357 ASN B 358 ASN B 369 GLN B 582 HIS C 91 ASN C 122 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 358 ASN C 369 GLN D 91 ASN D 122 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 358 ASN D 369 GLN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122998 restraints weight = 23547.923| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.92 r_work: 0.3037 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21040 Z= 0.135 Angle : 0.618 7.449 28504 Z= 0.314 Chirality : 0.040 0.194 3200 Planarity : 0.005 0.038 3512 Dihedral : 14.633 118.662 3888 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.28 % Allowed : 12.24 % Favored : 83.47 % 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: -1.77 (0.15), residues: 2440 helix: -1.05 (0.12), residues: 1468 sheet: -1.23 (0.46), residues: 124 loop : -1.06 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 492 TYR 0.010 0.002 TYR B 270 PHE 0.014 0.002 PHE C 478 TRP 0.012 0.001 TRP A 593 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00297 (21040) covalent geometry : angle 0.61811 (28504) hydrogen bonds : bond 0.04761 ( 1025) hydrogen bonds : angle 4.35801 ( 2919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 387 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6416 (t0) REVERT: A 96 MET cc_start: 0.7171 (mmt) cc_final: 0.6844 (mmm) REVERT: A 99 MET cc_start: 0.6432 (mtm) cc_final: 0.6188 (mtm) REVERT: A 133 VAL cc_start: 0.7684 (p) cc_final: 0.7365 (t) REVERT: A 185 HIS cc_start: 0.7685 (m90) cc_final: 0.7253 (m170) REVERT: A 300 LYS cc_start: 0.7942 (mppt) cc_final: 0.7567 (mmmm) REVERT: A 403 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: A 410 MET cc_start: 0.3376 (ttp) cc_final: 0.3068 (mmm) REVERT: A 484 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7186 (ttmm) REVERT: A 491 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6976 (mmm) REVERT: A 590 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: B 31 GLN cc_start: 0.7185 (tp40) cc_final: 0.6981 (tp-100) REVERT: B 90 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6406 (t0) REVERT: B 99 MET cc_start: 0.6451 (mtm) cc_final: 0.6080 (mtm) REVERT: B 133 VAL cc_start: 0.7683 (p) cc_final: 0.7370 (t) REVERT: B 225 HIS cc_start: 0.3982 (OUTLIER) cc_final: 0.3767 (p-80) REVERT: B 300 LYS cc_start: 0.7928 (mppt) cc_final: 0.7554 (mmmm) REVERT: B 357 ASN cc_start: 0.7347 (p0) cc_final: 0.7142 (p0) REVERT: B 403 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: B 484 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7246 (ttmm) REVERT: B 491 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6971 (mmm) REVERT: B 578 MET cc_start: 0.6570 (ttm) cc_final: 0.6364 (ttm) REVERT: B 590 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: C 90 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6415 (t0) REVERT: C 96 MET cc_start: 0.7129 (mmt) cc_final: 0.6796 (mmm) REVERT: C 99 MET cc_start: 0.6435 (mtm) cc_final: 0.6183 (mtm) REVERT: C 133 VAL cc_start: 0.7684 (p) cc_final: 0.7350 (t) REVERT: C 300 LYS cc_start: 0.7930 (mppt) cc_final: 0.7582 (mmmm) REVERT: C 403 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: C 484 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7107 (ttmm) REVERT: C 590 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: D 90 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6426 (t0) REVERT: D 96 MET cc_start: 0.7095 (mmt) cc_final: 0.6773 (mmm) REVERT: D 99 MET cc_start: 0.6433 (mtm) cc_final: 0.6187 (mtm) REVERT: D 133 VAL cc_start: 0.7695 (p) cc_final: 0.7363 (t) REVERT: D 300 LYS cc_start: 0.7929 (mppt) cc_final: 0.7572 (mmmm) REVERT: D 403 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: D 410 MET cc_start: 0.3373 (ttp) cc_final: 0.3057 (mmm) REVERT: D 484 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7155 (ttmm) outliers start: 91 outliers final: 29 residues processed: 443 average time/residue: 0.5944 time to fit residues: 296.4208 Evaluate side-chains 371 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 231 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 217 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 165 HIS A 201 HIS A 265 HIS A 365 ASN A 426 HIS A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 201 HIS B 265 HIS B 365 ASN B 426 HIS C 40 GLN C 165 HIS C 201 HIS C 265 HIS C 426 HIS C 572 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 165 HIS D 201 HIS D 265 HIS D 357 ASN D 365 ASN D 426 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119489 restraints weight = 23296.205| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.14 r_work: 0.2957 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21040 Z= 0.208 Angle : 0.700 9.483 28504 Z= 0.349 Chirality : 0.044 0.203 3200 Planarity : 0.005 0.035 3512 Dihedral : 14.536 116.122 3888 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.61 % Allowed : 15.49 % Favored : 79.90 % 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: -0.62 (0.16), residues: 2440 helix: 0.05 (0.13), residues: 1472 sheet: -1.01 (0.48), residues: 124 loop : -0.94 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 492 TYR 0.013 0.002 TYR D 89 PHE 0.016 0.002 PHE D 478 TRP 0.011 0.002 TRP D 593 HIS 0.008 0.002 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00497 (21040) covalent geometry : angle 0.69993 (28504) hydrogen bonds : bond 0.05050 ( 1025) hydrogen bonds : angle 4.30831 ( 2919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 342 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6607 (mp0) cc_final: 0.6301 (mp0) REVERT: A 90 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6466 (t0) REVERT: A 99 MET cc_start: 0.6360 (mtm) cc_final: 0.6052 (mtm) REVERT: A 137 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mm) REVERT: A 403 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: A 434 PHE cc_start: 0.7449 (t80) cc_final: 0.7210 (m-80) REVERT: A 590 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: B 90 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6460 (t0) REVERT: B 96 MET cc_start: 0.6848 (mmm) cc_final: 0.6541 (mmm) REVERT: B 99 MET cc_start: 0.6369 (mtm) cc_final: 0.6085 (mtm) REVERT: B 137 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7511 (mm) REVERT: B 381 LYS cc_start: 0.7271 (mmpt) cc_final: 0.6919 (ttmt) REVERT: B 403 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: B 578 MET cc_start: 0.6679 (ttm) cc_final: 0.6360 (ttm) REVERT: C 80 GLU cc_start: 0.6638 (mp0) cc_final: 0.6331 (mp0) REVERT: C 90 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6470 (t0) REVERT: C 96 MET cc_start: 0.7146 (mmt) cc_final: 0.6735 (mmm) REVERT: C 99 MET cc_start: 0.6358 (mtm) cc_final: 0.6080 (mtm) REVERT: C 137 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7514 (mm) REVERT: C 403 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: C 434 PHE cc_start: 0.7429 (t80) cc_final: 0.7196 (m-80) REVERT: C 578 MET cc_start: 0.6485 (ttm) cc_final: 0.6040 (ttm) REVERT: C 590 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: D 80 GLU cc_start: 0.6634 (mp0) cc_final: 0.6322 (mp0) REVERT: D 90 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6477 (t0) REVERT: D 96 MET cc_start: 0.7155 (mmt) cc_final: 0.6738 (mmm) REVERT: D 99 MET cc_start: 0.6377 (mtm) cc_final: 0.6107 (mtm) REVERT: D 137 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7508 (mm) REVERT: D 403 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: D 434 PHE cc_start: 0.7445 (t80) cc_final: 0.7199 (m-80) REVERT: D 590 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7178 (m-30) outliers start: 98 outliers final: 31 residues processed: 394 average time/residue: 0.5997 time to fit residues: 265.8584 Evaluate side-chains 362 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 316 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 126 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 265 HIS C 265 HIS C 582 HIS D 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122713 restraints weight = 23496.490| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.01 r_work: 0.3022 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21040 Z= 0.116 Angle : 0.585 9.579 28504 Z= 0.290 Chirality : 0.039 0.181 3200 Planarity : 0.004 0.034 3512 Dihedral : 13.159 112.573 3888 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.34 % Allowed : 18.27 % Favored : 78.39 % 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: 0.16 (0.17), residues: 2440 helix: 0.74 (0.13), residues: 1464 sheet: -0.97 (0.48), residues: 124 loop : -0.69 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 492 TYR 0.011 0.001 TYR A 524 PHE 0.013 0.001 PHE B 478 TRP 0.009 0.001 TRP D 593 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00257 (21040) covalent geometry : angle 0.58515 (28504) hydrogen bonds : bond 0.03939 ( 1025) hydrogen bonds : angle 3.87932 ( 2919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 348 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6665 (mp0) cc_final: 0.6366 (mp0) REVERT: A 90 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6478 (t0) REVERT: A 96 MET cc_start: 0.6778 (mmm) cc_final: 0.6398 (mmm) REVERT: A 99 MET cc_start: 0.6426 (mtm) cc_final: 0.6118 (mtm) REVERT: A 137 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7383 (mm) REVERT: A 185 HIS cc_start: 0.7617 (m90) cc_final: 0.7375 (m-70) REVERT: A 210 THR cc_start: 0.7980 (m) cc_final: 0.7709 (t) REVERT: A 300 LYS cc_start: 0.7988 (mppt) cc_final: 0.7663 (mmmm) REVERT: A 381 LYS cc_start: 0.7255 (mmpt) cc_final: 0.6954 (ttmt) REVERT: A 403 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 484 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6963 (ttmm) REVERT: B 90 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6481 (t0) REVERT: B 96 MET cc_start: 0.6929 (mmm) cc_final: 0.6700 (mmm) REVERT: B 99 MET cc_start: 0.6324 (mtm) cc_final: 0.6089 (mtm) REVERT: B 137 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7432 (mm) REVERT: B 185 HIS cc_start: 0.7629 (m90) cc_final: 0.7391 (m-70) REVERT: B 210 THR cc_start: 0.7974 (m) cc_final: 0.7702 (t) REVERT: B 300 LYS cc_start: 0.7975 (mppt) cc_final: 0.7623 (mmmm) REVERT: B 403 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: B 410 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3432 (mmt) REVERT: B 484 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6933 (ttmm) REVERT: B 578 MET cc_start: 0.6721 (ttm) cc_final: 0.6124 (ttm) REVERT: C 80 GLU cc_start: 0.6662 (mp0) cc_final: 0.6360 (mp0) REVERT: C 90 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6492 (t0) REVERT: C 96 MET cc_start: 0.7000 (mmt) cc_final: 0.6634 (mmm) REVERT: C 99 MET cc_start: 0.6306 (mtm) cc_final: 0.6086 (mtm) REVERT: C 137 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7401 (mm) REVERT: C 185 HIS cc_start: 0.7629 (m90) cc_final: 0.7398 (m-70) REVERT: C 210 THR cc_start: 0.7980 (m) cc_final: 0.7712 (t) REVERT: C 300 LYS cc_start: 0.8011 (mppt) cc_final: 0.7674 (mmmm) REVERT: C 381 LYS cc_start: 0.7287 (mmpt) cc_final: 0.6950 (ttmt) REVERT: C 403 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: C 410 MET cc_start: 0.4145 (tmm) cc_final: 0.3440 (mmt) REVERT: C 484 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7000 (ttmm) REVERT: C 590 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: D 80 GLU cc_start: 0.6652 (mp0) cc_final: 0.6348 (mp0) REVERT: D 90 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6503 (t0) REVERT: D 96 MET cc_start: 0.7013 (mmt) cc_final: 0.6642 (mmm) REVERT: D 99 MET cc_start: 0.6322 (mtm) cc_final: 0.6096 (mtm) REVERT: D 137 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7396 (mm) REVERT: D 185 HIS cc_start: 0.7627 (m90) cc_final: 0.7385 (m-70) REVERT: D 210 THR cc_start: 0.7973 (m) cc_final: 0.7696 (t) REVERT: D 300 LYS cc_start: 0.7982 (mppt) cc_final: 0.7670 (mmmm) REVERT: D 381 LYS cc_start: 0.7238 (mmpt) cc_final: 0.6959 (ttmt) REVERT: D 403 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: D 484 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6937 (ttmm) REVERT: D 574 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7689 (tt) REVERT: D 590 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6978 (m-30) outliers start: 71 outliers final: 12 residues processed: 387 average time/residue: 0.6018 time to fit residues: 262.0666 Evaluate side-chains 333 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 426 HIS C 265 HIS C 426 HIS D 265 HIS D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122770 restraints weight = 23188.641| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.93 r_work: 0.3005 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21040 Z= 0.131 Angle : 0.591 9.976 28504 Z= 0.293 Chirality : 0.040 0.197 3200 Planarity : 0.004 0.033 3512 Dihedral : 12.718 108.082 3888 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.53 % Allowed : 18.55 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2440 helix: 0.98 (0.14), residues: 1468 sheet: -1.02 (0.47), residues: 124 loop : -0.50 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 628 TYR 0.009 0.001 TYR A 524 PHE 0.017 0.002 PHE B 478 TRP 0.009 0.001 TRP A 593 HIS 0.008 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00303 (21040) covalent geometry : angle 0.59050 (28504) hydrogen bonds : bond 0.04000 ( 1025) hydrogen bonds : angle 3.83213 ( 2919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 0.708 Fit side-chains REVERT: A 80 GLU cc_start: 0.6704 (mp0) cc_final: 0.6435 (mp0) REVERT: A 90 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6485 (t0) REVERT: A 99 MET cc_start: 0.6360 (mtm) cc_final: 0.6127 (mtm) REVERT: A 137 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7479 (mm) REVERT: A 210 THR cc_start: 0.7945 (m) cc_final: 0.7634 (t) REVERT: A 300 LYS cc_start: 0.8021 (mppt) cc_final: 0.7635 (mmmm) REVERT: A 403 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 481 MET cc_start: 0.7125 (mmt) cc_final: 0.6701 (mtt) REVERT: A 571 LEU cc_start: 0.7428 (mm) cc_final: 0.7158 (mt) REVERT: A 578 MET cc_start: 0.6818 (ttm) cc_final: 0.6535 (ttm) REVERT: B 90 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6487 (t0) REVERT: B 96 MET cc_start: 0.6874 (mmm) cc_final: 0.6635 (mmm) REVERT: B 99 MET cc_start: 0.6421 (mtm) cc_final: 0.6045 (mtm) REVERT: B 137 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7448 (mm) REVERT: B 185 HIS cc_start: 0.7611 (m90) cc_final: 0.7368 (m-70) REVERT: B 210 THR cc_start: 0.7932 (m) cc_final: 0.7634 (t) REVERT: B 300 LYS cc_start: 0.8012 (mppt) cc_final: 0.7629 (mmmm) REVERT: B 381 LYS cc_start: 0.7278 (mmpt) cc_final: 0.6921 (ttmt) REVERT: B 410 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.3458 (mmt) REVERT: B 484 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7057 (ttmm) REVERT: C 80 GLU cc_start: 0.6689 (mp0) cc_final: 0.6411 (mp0) REVERT: C 90 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6482 (t0) REVERT: C 96 MET cc_start: 0.6974 (mmt) cc_final: 0.6706 (mmm) REVERT: C 99 MET cc_start: 0.6307 (mtm) cc_final: 0.6049 (mtm) REVERT: C 137 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7436 (mm) REVERT: C 185 HIS cc_start: 0.7596 (m90) cc_final: 0.7352 (m-70) REVERT: C 210 THR cc_start: 0.7947 (m) cc_final: 0.7644 (t) REVERT: C 300 LYS cc_start: 0.8006 (mppt) cc_final: 0.7653 (mmmm) REVERT: C 381 LYS cc_start: 0.7253 (mmpt) cc_final: 0.6943 (ttmt) REVERT: C 403 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: C 410 MET cc_start: 0.4086 (tmm) cc_final: 0.3377 (mmt) REVERT: C 590 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: C 591 GLU cc_start: 0.7437 (tt0) cc_final: 0.7157 (tp30) REVERT: D 35 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7439 (mp0) REVERT: D 80 GLU cc_start: 0.6677 (mp0) cc_final: 0.6417 (mp0) REVERT: D 90 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6495 (t0) REVERT: D 96 MET cc_start: 0.6987 (mmt) cc_final: 0.6710 (mmm) REVERT: D 99 MET cc_start: 0.6320 (mtm) cc_final: 0.6069 (mtm) REVERT: D 137 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7450 (mm) REVERT: D 210 THR cc_start: 0.7936 (m) cc_final: 0.7632 (t) REVERT: D 300 LYS cc_start: 0.8017 (mppt) cc_final: 0.7632 (mmmm) REVERT: D 381 LYS cc_start: 0.7221 (mmpt) cc_final: 0.6921 (ttmt) REVERT: D 403 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: D 590 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: D 591 GLU cc_start: 0.7427 (tt0) cc_final: 0.7106 (tp30) outliers start: 75 outliers final: 22 residues processed: 348 average time/residue: 0.6109 time to fit residues: 238.7537 Evaluate side-chains 334 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 426 HIS C 258 HIS C 265 HIS C 426 HIS D 265 HIS D 426 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119391 restraints weight = 23040.179| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.91 r_work: 0.2948 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21040 Z= 0.241 Angle : 0.714 9.686 28504 Z= 0.355 Chirality : 0.046 0.218 3200 Planarity : 0.005 0.041 3512 Dihedral : 13.463 108.762 3888 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.18 % Allowed : 17.42 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2440 helix: 0.79 (0.13), residues: 1464 sheet: -1.09 (0.46), residues: 124 loop : -0.64 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 33 TYR 0.015 0.003 TYR D 89 PHE 0.021 0.003 PHE B 478 TRP 0.011 0.002 TRP C 593 HIS 0.009 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00584 (21040) covalent geometry : angle 0.71376 (28504) hydrogen bonds : bond 0.04809 ( 1025) hydrogen bonds : angle 4.19127 ( 2919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 331 time to evaluate : 0.824 Fit side-chains REVERT: A 80 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 90 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6533 (t0) REVERT: A 99 MET cc_start: 0.6582 (mtm) cc_final: 0.6158 (mtm) REVERT: A 137 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7460 (mm) REVERT: A 177 GLU cc_start: 0.7586 (pm20) cc_final: 0.7367 (pm20) REVERT: A 185 HIS cc_start: 0.7648 (m90) cc_final: 0.7444 (m-70) REVERT: A 225 HIS cc_start: 0.3883 (OUTLIER) cc_final: 0.3497 (p-80) REVERT: A 381 LYS cc_start: 0.7269 (mmpt) cc_final: 0.6906 (ttmt) REVERT: A 403 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 434 PHE cc_start: 0.7469 (t80) cc_final: 0.7205 (m-80) REVERT: A 481 MET cc_start: 0.7327 (mmt) cc_final: 0.6856 (mmp) REVERT: A 578 MET cc_start: 0.6930 (ttm) cc_final: 0.6571 (ttm) REVERT: B 80 GLU cc_start: 0.6598 (mp0) cc_final: 0.6308 (mp0) REVERT: B 90 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6530 (t0) REVERT: B 96 MET cc_start: 0.6759 (mmm) cc_final: 0.6555 (mmm) REVERT: B 99 MET cc_start: 0.6485 (mtm) cc_final: 0.6157 (mtm) REVERT: B 137 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7451 (mm) REVERT: B 185 HIS cc_start: 0.7638 (m90) cc_final: 0.7436 (m-70) REVERT: B 294 GLU cc_start: 0.7663 (mp0) cc_final: 0.7232 (mp0) REVERT: B 403 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: B 410 MET cc_start: 0.4179 (OUTLIER) cc_final: 0.3343 (mmm) REVERT: C 80 GLU cc_start: 0.6753 (mp0) cc_final: 0.6469 (mp0) REVERT: C 90 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6520 (t0) REVERT: C 96 MET cc_start: 0.6939 (mmt) cc_final: 0.6632 (mmm) REVERT: C 137 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7480 (mm) REVERT: C 225 HIS cc_start: 0.3885 (OUTLIER) cc_final: 0.3505 (p-80) REVERT: C 403 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: C 410 MET cc_start: 0.4040 (OUTLIER) cc_final: 0.3228 (mmm) REVERT: C 434 PHE cc_start: 0.7438 (t80) cc_final: 0.7191 (m-80) REVERT: C 590 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: C 591 GLU cc_start: 0.7469 (tt0) cc_final: 0.7200 (tp30) REVERT: C 592 LEU cc_start: 0.7951 (mt) cc_final: 0.7727 (mp) REVERT: D 80 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: D 90 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6530 (t0) REVERT: D 96 MET cc_start: 0.6954 (mmt) cc_final: 0.6638 (mmm) REVERT: D 137 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7430 (mm) REVERT: D 225 HIS cc_start: 0.3886 (OUTLIER) cc_final: 0.3497 (p-80) REVERT: D 403 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: D 434 PHE cc_start: 0.7441 (t80) cc_final: 0.7196 (m-80) REVERT: D 481 MET cc_start: 0.7303 (mmt) cc_final: 0.6545 (mtt) REVERT: D 591 GLU cc_start: 0.7394 (tt0) cc_final: 0.7123 (tp30) outliers start: 110 outliers final: 34 residues processed: 395 average time/residue: 0.6116 time to fit residues: 271.7809 Evaluate side-chains 367 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 187 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS B 265 HIS B 426 HIS C 265 HIS C 426 HIS D 265 HIS D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123806 restraints weight = 23222.300| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.93 r_work: 0.2982 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21040 Z= 0.127 Angle : 0.606 7.937 28504 Z= 0.298 Chirality : 0.040 0.194 3200 Planarity : 0.004 0.033 3512 Dihedral : 12.385 103.433 3888 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.77 % Allowed : 19.63 % Favored : 76.60 % 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: 0.66 (0.17), residues: 2440 helix: 1.13 (0.14), residues: 1460 sheet: -1.02 (0.47), residues: 124 loop : -0.43 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 492 TYR 0.011 0.001 TYR A 524 PHE 0.015 0.001 PHE B 478 TRP 0.006 0.001 TRP D 613 HIS 0.009 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00291 (21040) covalent geometry : angle 0.60602 (28504) hydrogen bonds : bond 0.03901 ( 1025) hydrogen bonds : angle 3.85693 ( 2919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 320 time to evaluate : 0.733 Fit side-chains REVERT: A 35 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7302 (mp0) REVERT: A 90 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6509 (t0) REVERT: A 96 MET cc_start: 0.6776 (mmm) cc_final: 0.6517 (mmm) REVERT: A 99 MET cc_start: 0.6593 (mtm) cc_final: 0.6218 (mtm) REVERT: A 137 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7448 (mm) REVERT: A 185 HIS cc_start: 0.7638 (m90) cc_final: 0.7420 (m-70) REVERT: A 300 LYS cc_start: 0.8027 (mppt) cc_final: 0.7671 (mmmm) REVERT: A 381 LYS cc_start: 0.7252 (mmpt) cc_final: 0.6903 (ttmt) REVERT: A 403 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: A 410 MET cc_start: 0.3525 (ttp) cc_final: 0.3177 (mmt) REVERT: A 481 MET cc_start: 0.7204 (mmt) cc_final: 0.6643 (mmp) REVERT: A 578 MET cc_start: 0.6732 (ttm) cc_final: 0.6384 (ttm) REVERT: B 35 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7255 (mp0) REVERT: B 80 GLU cc_start: 0.6670 (mp0) cc_final: 0.6464 (mp0) REVERT: B 90 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6511 (t0) REVERT: B 99 MET cc_start: 0.6482 (mtm) cc_final: 0.6171 (mtm) REVERT: B 137 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (mm) REVERT: B 185 HIS cc_start: 0.7639 (m90) cc_final: 0.7422 (m-70) REVERT: B 294 GLU cc_start: 0.7766 (mp0) cc_final: 0.7351 (mp0) REVERT: B 300 LYS cc_start: 0.7983 (mppt) cc_final: 0.7636 (mmmm) REVERT: B 381 LYS cc_start: 0.7343 (mmpt) cc_final: 0.6962 (ttmt) REVERT: B 403 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: B 410 MET cc_start: 0.4319 (OUTLIER) cc_final: 0.3477 (mmt) REVERT: B 481 MET cc_start: 0.7015 (mmt) cc_final: 0.6293 (mtt) REVERT: C 35 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7389 (mp0) REVERT: C 137 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7453 (mm) REVERT: C 185 HIS cc_start: 0.7629 (m90) cc_final: 0.7419 (m-70) REVERT: C 300 LYS cc_start: 0.7997 (mppt) cc_final: 0.7682 (mmmm) REVERT: C 381 LYS cc_start: 0.7311 (mmpt) cc_final: 0.6935 (ttmt) REVERT: C 403 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: C 410 MET cc_start: 0.4241 (tmm) cc_final: 0.3452 (mmt) REVERT: C 481 MET cc_start: 0.7002 (mmt) cc_final: 0.6302 (mtt) REVERT: C 491 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7084 (mmt) REVERT: C 578 MET cc_start: 0.6736 (ttm) cc_final: 0.6306 (ttm) REVERT: C 591 GLU cc_start: 0.7399 (tt0) cc_final: 0.7193 (tp30) REVERT: D 35 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7344 (mp0) REVERT: D 96 MET cc_start: 0.6914 (mmt) cc_final: 0.6710 (mmm) REVERT: D 137 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7458 (mm) REVERT: D 300 LYS cc_start: 0.8016 (mppt) cc_final: 0.7673 (mmmm) REVERT: D 345 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: D 381 LYS cc_start: 0.7291 (mmpt) cc_final: 0.6924 (ttmt) REVERT: D 403 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: D 410 MET cc_start: 0.3532 (ttp) cc_final: 0.3159 (mmt) REVERT: D 481 MET cc_start: 0.7108 (mmt) cc_final: 0.6351 (mtt) REVERT: D 578 MET cc_start: 0.6955 (ttm) cc_final: 0.6570 (mtt) REVERT: D 591 GLU cc_start: 0.7331 (tt0) cc_final: 0.7045 (mm-30) outliers start: 80 outliers final: 28 residues processed: 363 average time/residue: 0.6052 time to fit residues: 247.0174 Evaluate side-chains 341 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 12 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS B 265 HIS B 426 HIS C 265 HIS C 426 HIS D 265 HIS D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121203 restraints weight = 23252.418| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.94 r_work: 0.2988 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21040 Z= 0.149 Angle : 0.629 8.796 28504 Z= 0.309 Chirality : 0.041 0.200 3200 Planarity : 0.004 0.033 3512 Dihedral : 12.241 102.444 3888 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.30 % Allowed : 20.39 % Favored : 76.32 % 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: 0.66 (0.17), residues: 2440 helix: 1.14 (0.14), residues: 1464 sheet: -1.01 (0.48), residues: 124 loop : -0.45 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 492 TYR 0.012 0.002 TYR B 216 PHE 0.020 0.002 PHE B 478 TRP 0.008 0.001 TRP A 593 HIS 0.009 0.002 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00352 (21040) covalent geometry : angle 0.62870 (28504) hydrogen bonds : bond 0.04113 ( 1025) hydrogen bonds : angle 3.89100 ( 2919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 312 time to evaluate : 0.656 Fit side-chains REVERT: A 35 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7242 (mp0) REVERT: A 80 GLU cc_start: 0.6607 (mp0) cc_final: 0.5911 (pm20) REVERT: A 90 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6500 (t0) REVERT: A 96 MET cc_start: 0.6818 (mmm) cc_final: 0.6591 (mmm) REVERT: A 99 MET cc_start: 0.6522 (mtm) cc_final: 0.6205 (mtm) REVERT: A 137 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7442 (mm) REVERT: A 185 HIS cc_start: 0.7621 (m90) cc_final: 0.7420 (m-70) REVERT: A 300 LYS cc_start: 0.8028 (mppt) cc_final: 0.7641 (mmmm) REVERT: A 381 LYS cc_start: 0.7270 (mmpt) cc_final: 0.6833 (ttmt) REVERT: A 410 MET cc_start: 0.3562 (ttp) cc_final: 0.3112 (mmt) REVERT: A 481 MET cc_start: 0.7164 (mmt) cc_final: 0.6630 (mmp) REVERT: A 578 MET cc_start: 0.6760 (ttm) cc_final: 0.6404 (ttm) REVERT: B 35 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7230 (mp0) REVERT: B 80 GLU cc_start: 0.6677 (mp0) cc_final: 0.6449 (mp0) REVERT: B 90 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6418 (t0) REVERT: B 96 MET cc_start: 0.7171 (mmm) cc_final: 0.6725 (mmm) REVERT: B 137 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7439 (mm) REVERT: B 185 HIS cc_start: 0.7635 (m90) cc_final: 0.7433 (m-70) REVERT: B 294 GLU cc_start: 0.7687 (mp0) cc_final: 0.7274 (mp0) REVERT: B 300 LYS cc_start: 0.8004 (mppt) cc_final: 0.7631 (mmmm) REVERT: B 381 LYS cc_start: 0.7335 (mmpt) cc_final: 0.6977 (ttmt) REVERT: B 403 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 410 MET cc_start: 0.4311 (OUTLIER) cc_final: 0.3490 (mmt) REVERT: B 481 MET cc_start: 0.7145 (mmt) cc_final: 0.6417 (mtt) REVERT: C 35 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7218 (mp0) REVERT: C 80 GLU cc_start: 0.6597 (mp0) cc_final: 0.5913 (pm20) REVERT: C 90 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6473 (t0) REVERT: C 137 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 185 HIS cc_start: 0.7633 (m90) cc_final: 0.7432 (m-70) REVERT: C 300 LYS cc_start: 0.8024 (mppt) cc_final: 0.7646 (mmmm) REVERT: C 381 LYS cc_start: 0.7284 (mmpt) cc_final: 0.6851 (ttmt) REVERT: C 410 MET cc_start: 0.4237 (tmm) cc_final: 0.3480 (mmt) REVERT: C 481 MET cc_start: 0.7180 (mmt) cc_final: 0.6463 (mtt) REVERT: C 578 MET cc_start: 0.6781 (ttm) cc_final: 0.6415 (ttm) REVERT: C 591 GLU cc_start: 0.7342 (tt0) cc_final: 0.7034 (mm-30) REVERT: C 592 LEU cc_start: 0.7842 (mt) cc_final: 0.7627 (mp) REVERT: D 35 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7306 (mp0) REVERT: D 38 LEU cc_start: 0.8832 (mp) cc_final: 0.8546 (mt) REVERT: D 80 GLU cc_start: 0.6606 (mp0) cc_final: 0.5894 (pm20) REVERT: D 90 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6479 (t0) REVERT: D 96 MET cc_start: 0.6896 (mmt) cc_final: 0.6637 (mmm) REVERT: D 137 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7446 (mm) REVERT: D 210 THR cc_start: 0.7797 (m) cc_final: 0.7461 (t) REVERT: D 300 LYS cc_start: 0.8024 (mppt) cc_final: 0.7645 (mmmm) REVERT: D 345 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8094 (mtt) REVERT: D 381 LYS cc_start: 0.7283 (mmpt) cc_final: 0.6847 (ttmt) REVERT: D 410 MET cc_start: 0.3683 (ttp) cc_final: 0.3163 (mmt) REVERT: D 481 MET cc_start: 0.7121 (mmt) cc_final: 0.6399 (mtt) REVERT: D 578 MET cc_start: 0.6961 (ttm) cc_final: 0.6584 (mtt) REVERT: D 591 GLU cc_start: 0.7297 (tt0) cc_final: 0.7029 (mm-30) outliers start: 70 outliers final: 32 residues processed: 360 average time/residue: 0.5918 time to fit residues: 240.4614 Evaluate side-chains 343 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 227 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS B 265 HIS B 426 HIS C 265 HIS C 426 HIS D 265 HIS D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123508 restraints weight = 23116.240| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.93 r_work: 0.3011 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21040 Z= 0.125 Angle : 0.604 9.197 28504 Z= 0.295 Chirality : 0.040 0.192 3200 Planarity : 0.004 0.033 3512 Dihedral : 11.780 99.656 3888 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.39 % Allowed : 20.57 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2440 helix: 1.24 (0.14), residues: 1464 sheet: -0.98 (0.48), residues: 124 loop : -0.35 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 492 TYR 0.012 0.001 TYR B 216 PHE 0.017 0.001 PHE B 478 TRP 0.006 0.001 TRP C 593 HIS 0.010 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00288 (21040) covalent geometry : angle 0.60412 (28504) hydrogen bonds : bond 0.03833 ( 1025) hydrogen bonds : angle 3.79642 ( 2919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 0.755 Fit side-chains REVERT: A 35 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7246 (mp0) REVERT: A 80 GLU cc_start: 0.6634 (mp0) cc_final: 0.6006 (pm20) REVERT: A 90 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6401 (t0) REVERT: A 96 MET cc_start: 0.6824 (mmm) cc_final: 0.6560 (mmm) REVERT: A 99 MET cc_start: 0.6554 (mtm) cc_final: 0.6246 (mtm) REVERT: A 137 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7442 (mm) REVERT: A 185 HIS cc_start: 0.7621 (m90) cc_final: 0.7410 (m-70) REVERT: A 210 THR cc_start: 0.7786 (m) cc_final: 0.7552 (t) REVERT: A 300 LYS cc_start: 0.8010 (mppt) cc_final: 0.7622 (mmmm) REVERT: A 381 LYS cc_start: 0.7312 (mmpt) cc_final: 0.6967 (ttmt) REVERT: A 403 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: A 410 MET cc_start: 0.3513 (ttp) cc_final: 0.3094 (mmt) REVERT: A 481 MET cc_start: 0.7077 (mmt) cc_final: 0.6517 (mmp) REVERT: A 578 MET cc_start: 0.6663 (ttm) cc_final: 0.6333 (ttm) REVERT: B 35 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7200 (mp0) REVERT: B 80 GLU cc_start: 0.6759 (mp0) cc_final: 0.6534 (mp0) REVERT: B 90 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6387 (t0) REVERT: B 96 MET cc_start: 0.7091 (mmm) cc_final: 0.6725 (mmm) REVERT: B 137 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7455 (mm) REVERT: B 185 HIS cc_start: 0.7631 (m90) cc_final: 0.7421 (m-70) REVERT: B 210 THR cc_start: 0.7761 (m) cc_final: 0.7439 (t) REVERT: B 294 GLU cc_start: 0.7726 (mp0) cc_final: 0.7332 (mp0) REVERT: B 300 LYS cc_start: 0.7980 (mppt) cc_final: 0.7615 (mmmm) REVERT: B 381 LYS cc_start: 0.7341 (mmpt) cc_final: 0.6960 (ttmt) REVERT: B 403 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: B 410 MET cc_start: 0.4421 (OUTLIER) cc_final: 0.3629 (mmt) REVERT: B 481 MET cc_start: 0.6965 (mmt) cc_final: 0.6251 (mtt) REVERT: C 35 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7284 (mp0) REVERT: C 80 GLU cc_start: 0.6656 (mp0) cc_final: 0.6063 (pm20) REVERT: C 90 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6369 (t0) REVERT: C 137 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7411 (mm) REVERT: C 185 HIS cc_start: 0.7613 (m90) cc_final: 0.7406 (m-70) REVERT: C 210 THR cc_start: 0.7841 (m) cc_final: 0.7607 (t) REVERT: C 300 LYS cc_start: 0.8004 (mppt) cc_final: 0.7634 (mmmm) REVERT: C 381 LYS cc_start: 0.7320 (mmpt) cc_final: 0.6977 (ttmt) REVERT: C 403 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: C 410 MET cc_start: 0.4270 (tmm) cc_final: 0.3527 (mmt) REVERT: C 481 MET cc_start: 0.7093 (mmt) cc_final: 0.6353 (mtt) REVERT: C 578 MET cc_start: 0.6645 (ttm) cc_final: 0.6262 (ttm) REVERT: C 591 GLU cc_start: 0.7314 (tt0) cc_final: 0.7020 (mm-30) REVERT: D 35 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7301 (mp0) REVERT: D 38 LEU cc_start: 0.8848 (mp) cc_final: 0.8569 (mt) REVERT: D 80 GLU cc_start: 0.6668 (mp0) cc_final: 0.6042 (pm20) REVERT: D 90 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6411 (t0) REVERT: D 137 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7448 (mm) REVERT: D 210 THR cc_start: 0.7834 (m) cc_final: 0.7599 (t) REVERT: D 300 LYS cc_start: 0.8004 (mppt) cc_final: 0.7624 (mmmm) REVERT: D 345 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: D 381 LYS cc_start: 0.7308 (mmpt) cc_final: 0.6969 (ttmt) REVERT: D 403 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: D 410 MET cc_start: 0.3459 (ttp) cc_final: 0.3053 (mmt) REVERT: D 481 MET cc_start: 0.6991 (mmt) cc_final: 0.6285 (mtt) REVERT: D 578 MET cc_start: 0.6902 (ttm) cc_final: 0.6533 (mtt) outliers start: 72 outliers final: 34 residues processed: 366 average time/residue: 0.5990 time to fit residues: 247.0798 Evaluate side-chains 346 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 205 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 199 optimal weight: 0.0470 chunk 195 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 426 HIS B 265 HIS B 426 HIS C 265 HIS ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS D 265 HIS D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122981 restraints weight = 23274.453| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.93 r_work: 0.3000 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21040 Z= 0.136 Angle : 0.627 9.659 28504 Z= 0.307 Chirality : 0.041 0.235 3200 Planarity : 0.004 0.033 3512 Dihedral : 11.706 99.462 3888 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.82 % Allowed : 21.52 % Favored : 75.66 % 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: 0.82 (0.17), residues: 2440 helix: 1.23 (0.14), residues: 1460 sheet: -0.98 (0.48), residues: 124 loop : -0.30 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 492 TYR 0.014 0.002 TYR B 216 PHE 0.021 0.002 PHE C 478 TRP 0.007 0.001 TRP C 593 HIS 0.010 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00319 (21040) covalent geometry : angle 0.62659 (28504) hydrogen bonds : bond 0.03931 ( 1025) hydrogen bonds : angle 3.82929 ( 2919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 0.740 Fit side-chains REVERT: A 35 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7227 (mp0) REVERT: A 80 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6052 (pm20) REVERT: A 90 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6403 (t0) REVERT: A 96 MET cc_start: 0.6811 (mmm) cc_final: 0.6440 (mmt) REVERT: A 99 MET cc_start: 0.6565 (mtm) cc_final: 0.6174 (mtm) REVERT: A 137 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7438 (mm) REVERT: A 185 HIS cc_start: 0.7613 (m90) cc_final: 0.7398 (m-70) REVERT: A 210 THR cc_start: 0.7802 (m) cc_final: 0.7487 (t) REVERT: A 300 LYS cc_start: 0.7981 (mppt) cc_final: 0.7578 (mmmm) REVERT: A 381 LYS cc_start: 0.7299 (mmpt) cc_final: 0.6882 (ttmt) REVERT: A 403 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: A 410 MET cc_start: 0.3511 (ttp) cc_final: 0.2991 (mmt) REVERT: A 481 MET cc_start: 0.6997 (mmt) cc_final: 0.6443 (mmp) REVERT: A 578 MET cc_start: 0.6643 (ttm) cc_final: 0.6408 (ttm) REVERT: B 35 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7193 (mp0) REVERT: B 38 LEU cc_start: 0.8846 (mp) cc_final: 0.8558 (mt) REVERT: B 80 GLU cc_start: 0.6769 (mp0) cc_final: 0.6547 (mp0) REVERT: B 90 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6407 (t0) REVERT: B 137 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7436 (mm) REVERT: B 185 HIS cc_start: 0.7618 (m90) cc_final: 0.7403 (m-70) REVERT: B 210 THR cc_start: 0.7804 (m) cc_final: 0.7482 (t) REVERT: B 294 GLU cc_start: 0.7712 (mp0) cc_final: 0.7306 (mp0) REVERT: B 300 LYS cc_start: 0.7978 (mppt) cc_final: 0.7585 (mmmm) REVERT: B 345 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8069 (mtm) REVERT: B 381 LYS cc_start: 0.7313 (mmpt) cc_final: 0.6987 (ttmt) REVERT: B 403 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 410 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3632 (mmt) REVERT: B 481 MET cc_start: 0.7014 (mmt) cc_final: 0.6314 (mtt) REVERT: C 35 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7281 (mp0) REVERT: C 80 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: C 137 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7410 (mm) REVERT: C 185 HIS cc_start: 0.7626 (m90) cc_final: 0.7412 (m-70) REVERT: C 210 THR cc_start: 0.7789 (m) cc_final: 0.7455 (t) REVERT: C 300 LYS cc_start: 0.8007 (mppt) cc_final: 0.7610 (mmmm) REVERT: C 403 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: C 410 MET cc_start: 0.4279 (tmm) cc_final: 0.3519 (mmt) REVERT: C 481 MET cc_start: 0.7139 (mmt) cc_final: 0.6414 (mtt) REVERT: C 578 MET cc_start: 0.6629 (ttm) cc_final: 0.6120 (mtt) REVERT: C 591 GLU cc_start: 0.7315 (tt0) cc_final: 0.7022 (mm-30) REVERT: C 592 LEU cc_start: 0.7800 (mt) cc_final: 0.7576 (mp) REVERT: D 35 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7295 (mp0) REVERT: D 38 LEU cc_start: 0.8844 (mp) cc_final: 0.8566 (mt) REVERT: D 80 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6009 (pm20) REVERT: D 90 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6397 (t0) REVERT: D 137 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (mm) REVERT: D 176 GLU cc_start: 0.7393 (pm20) cc_final: 0.7130 (pm20) REVERT: D 210 THR cc_start: 0.7781 (m) cc_final: 0.7452 (t) REVERT: D 300 LYS cc_start: 0.7970 (mppt) cc_final: 0.7589 (mmmm) REVERT: D 345 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: D 381 LYS cc_start: 0.7324 (mmpt) cc_final: 0.6921 (ttmt) REVERT: D 403 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 410 MET cc_start: 0.3511 (ttp) cc_final: 0.2974 (mmt) REVERT: D 481 MET cc_start: 0.6990 (mmt) cc_final: 0.6316 (mtt) REVERT: D 578 MET cc_start: 0.6865 (ttm) cc_final: 0.6489 (mtt) outliers start: 60 outliers final: 32 residues processed: 356 average time/residue: 0.5962 time to fit residues: 239.1311 Evaluate side-chains 355 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 306 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 140 optimal weight: 0.0870 chunk 86 optimal weight: 7.9990 chunk 157 optimal weight: 0.0970 chunk 171 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 chunk 138 optimal weight: 0.2980 chunk 208 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS B 265 HIS B 426 HIS C 265 HIS ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS D 265 HIS ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126319 restraints weight = 23421.509| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.05 r_work: 0.3062 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21040 Z= 0.109 Angle : 0.590 9.134 28504 Z= 0.286 Chirality : 0.039 0.273 3200 Planarity : 0.004 0.033 3512 Dihedral : 11.208 95.183 3888 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.26 % Allowed : 22.27 % Favored : 75.47 % 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: 1.08 (0.18), residues: 2440 helix: 1.41 (0.14), residues: 1456 sheet: -0.98 (0.49), residues: 124 loop : -0.10 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 492 TYR 0.012 0.001 TYR C 216 PHE 0.018 0.001 PHE C 478 TRP 0.005 0.001 TRP A 462 HIS 0.010 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00238 (21040) covalent geometry : angle 0.58958 (28504) hydrogen bonds : bond 0.03507 ( 1025) hydrogen bonds : angle 3.66921 ( 2919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6816.16 seconds wall clock time: 116 minutes 44.43 seconds (7004.43 seconds total)