Starting phenix.real_space_refine on Fri Jun 13 09:52:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.map" model { file = "/net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc6_44425/06_2025/9bc6_44425.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9868 2.51 5 N 2468 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14972 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3695 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 167 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'PCW': 2, 'PFL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Restraints were copied for chains: B, C, D Time building chain proxies: 9.54, per 1000 atoms: 0.64 Number of scatterers: 14972 At special positions: 0 Unit cell: (115.868, 115.868, 115.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2528 8.00 N 2468 7.00 C 9868 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 71.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.816A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.672A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.865A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR A 545 " --> pdb=" O CYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.816A pdb=" N LEU B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.672A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.831A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR B 545 " --> pdb=" O CYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.815A pdb=" N LEU C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.671A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.861A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR C 545 " --> pdb=" O CYS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.944A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.816A pdb=" N LEU D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.607A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.671A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.830A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.304A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 288 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.807A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.866A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.560A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 removed outlier: 4.014A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.860A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 545 removed outlier: 4.232A pdb=" N THR D 545 " --> pdb=" O CYS D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 575 removed outlier: 3.945A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.529A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.644A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.643A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.645A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.440A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.644A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.439A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2871 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: 4.77 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2288 1.28 - 1.41: 4222 1.41 - 1.55: 8610 1.55 - 1.68: 20 1.68 - 1.82: 188 Bond restraints: 15328 Sorted by residual: bond pdb=" C ARG D 142 " pdb=" O ARG D 142 " ideal model delta sigma weight residual 1.237 1.144 0.092 1.19e-02 7.06e+03 6.01e+01 bond pdb=" C ARG A 142 " pdb=" O ARG A 142 " ideal model delta sigma weight residual 1.237 1.145 0.091 1.19e-02 7.06e+03 5.91e+01 bond pdb=" C ARG C 142 " pdb=" O ARG C 142 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.19e-02 7.06e+03 5.86e+01 bond pdb=" C ARG B 142 " pdb=" O ARG B 142 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.19e-02 7.06e+03 5.85e+01 bond pdb=" CA ARG C 142 " pdb=" CB ARG C 142 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.59e-02 3.96e+03 1.67e+01 ... (remaining 15323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 17809 2.55 - 5.10: 2850 5.10 - 7.64: 117 7.64 - 10.19: 4 10.19 - 12.74: 8 Bond angle restraints: 20788 Sorted by residual: angle pdb=" C ILE A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 angle pdb=" C ILE C 159 " pdb=" N ILE C 160 " pdb=" CA ILE C 160 " ideal model delta sigma weight residual 120.33 124.36 -4.03 8.00e-01 1.56e+00 2.54e+01 angle pdb=" C ILE D 159 " pdb=" N ILE D 160 " pdb=" CA ILE D 160 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C ILE B 159 " pdb=" N ILE B 160 " pdb=" CA ILE B 160 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" CB HIS D 437 " pdb=" CG HIS D 437 " pdb=" CD2 HIS D 437 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 20783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8382 17.07 - 34.14: 502 34.14 - 51.21: 96 51.21 - 68.27: 24 68.27 - 85.34: 4 Dihedral angle restraints: 9008 sinusoidal: 3304 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR C 361 " pdb=" C TYR C 361 " pdb=" N GLY C 362 " pdb=" CA GLY C 362 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual 180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TYR A 361 " pdb=" C TYR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1457 0.075 - 0.149: 673 0.149 - 0.224: 162 0.224 - 0.299: 28 0.299 - 0.373: 28 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ARG B 258 " pdb=" N ARG B 258 " pdb=" C ARG B 258 " pdb=" CB ARG B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA ARG D 258 " pdb=" N ARG D 258 " pdb=" C ARG D 258 " pdb=" CB ARG D 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ARG A 258 " pdb=" N ARG A 258 " pdb=" C ARG A 258 " pdb=" CB ARG A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2345 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 281 " 0.158 2.00e-02 2.50e+03 7.47e-02 1.39e+02 pdb=" CG TRP B 281 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 281 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP B 281 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 281 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP B 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 281 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 281 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 281 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP B 281 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.158 2.00e-02 2.50e+03 7.46e-02 1.39e+02 pdb=" CG TRP A 281 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " -0.158 2.00e-02 2.50e+03 7.45e-02 1.39e+02 pdb=" CG TRP C 281 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " -0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1317 2.78 - 3.31: 15196 3.31 - 3.84: 24045 3.84 - 4.37: 29358 4.37 - 4.90: 49284 Nonbonded interactions: 119200 Sorted by model distance: nonbonded pdb=" O LEU C 254 " pdb=" NE ARG C 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU D 254 " pdb=" NE ARG D 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU A 254 " pdb=" NE ARG A 258 " model vdw 2.247 3.120 nonbonded pdb=" O LEU B 254 " pdb=" NE ARG B 258 " model vdw 2.248 3.120 nonbonded pdb=" ND1 HIS D 310 " pdb=" OH TYR D 345 " model vdw 2.381 3.120 ... (remaining 119195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 94 through 586 or resid 702)) selection = (chain 'B' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'C' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'D' and (resid 94 through 586 or (resid 702 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 78.040 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 34.730 Find NCS groups from input model: 0.830 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.012 0.092 15328 Z= 0.712 Angle : 1.767 12.741 20788 Z= 1.208 Chirality : 0.093 0.373 2348 Planarity : 0.014 0.092 2596 Dihedral : 12.254 85.343 5320 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.56 % Allowed : 2.51 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1920 helix: -0.35 (0.13), residues: 1288 sheet: -0.78 (0.47), residues: 112 loop : -0.00 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.027 TRP B 281 HIS 0.019 0.005 HIS D 286 PHE 0.066 0.013 PHE A 186 TYR 0.119 0.022 TYR D 407 ARG 0.008 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.19323 ( 989) hydrogen bonds : angle 6.89939 ( 2871) covalent geometry : bond 0.01157 (15328) covalent geometry : angle 1.76655 (20788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 1.915 Fit side-chains REVERT: A 101 MET cc_start: 0.6371 (mmt) cc_final: 0.5967 (tpp) REVERT: A 195 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5852 (mmp-170) REVERT: A 283 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6314 (mm-30) REVERT: A 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3847 (tpt) REVERT: A 304 MET cc_start: 0.8000 (tpp) cc_final: 0.7668 (tpp) REVERT: A 308 LEU cc_start: 0.7955 (mt) cc_final: 0.7632 (mm) REVERT: A 343 LYS cc_start: 0.7879 (mtmm) cc_final: 0.6899 (tptm) REVERT: A 388 MET cc_start: 0.8256 (mmm) cc_final: 0.7978 (mmt) REVERT: A 401 ASP cc_start: 0.6121 (p0) cc_final: 0.5548 (t0) REVERT: A 408 GLN cc_start: 0.7768 (mm110) cc_final: 0.7452 (mm-40) REVERT: A 411 TYR cc_start: 0.6253 (t80) cc_final: 0.5859 (t80) REVERT: A 415 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7129 (mt-10) REVERT: A 459 GLU cc_start: 0.8410 (pt0) cc_final: 0.7656 (mt-10) REVERT: A 483 PHE cc_start: 0.7226 (t80) cc_final: 0.6773 (t80) REVERT: B 101 MET cc_start: 0.6374 (mmt) cc_final: 0.5970 (tpp) REVERT: B 195 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5845 (mmp-170) REVERT: B 283 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6334 (mm-30) REVERT: B 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3836 (tpt) REVERT: B 304 MET cc_start: 0.8015 (tpp) cc_final: 0.7675 (tpp) REVERT: B 308 LEU cc_start: 0.7974 (mt) cc_final: 0.7653 (mm) REVERT: B 343 LYS cc_start: 0.7866 (mtmm) cc_final: 0.6882 (tptm) REVERT: B 388 MET cc_start: 0.8262 (mmm) cc_final: 0.7982 (mmt) REVERT: B 401 ASP cc_start: 0.6087 (p0) cc_final: 0.5547 (t0) REVERT: B 408 GLN cc_start: 0.7783 (mm110) cc_final: 0.7472 (mm-40) REVERT: B 411 TYR cc_start: 0.6259 (t80) cc_final: 0.5863 (t80) REVERT: B 415 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7138 (mt-10) REVERT: B 459 GLU cc_start: 0.8399 (pt0) cc_final: 0.7654 (mt-10) REVERT: B 483 PHE cc_start: 0.7240 (t80) cc_final: 0.6843 (t80) REVERT: C 101 MET cc_start: 0.6359 (mmt) cc_final: 0.5959 (tpp) REVERT: C 195 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5855 (mmp-170) REVERT: C 283 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6318 (mm-30) REVERT: C 287 MET cc_start: 0.5023 (ttp) cc_final: 0.3831 (tpt) REVERT: C 304 MET cc_start: 0.8030 (tpp) cc_final: 0.7702 (tpp) REVERT: C 308 LEU cc_start: 0.7967 (mt) cc_final: 0.7651 (mm) REVERT: C 343 LYS cc_start: 0.7855 (mtmm) cc_final: 0.6876 (tptm) REVERT: C 388 MET cc_start: 0.8254 (mmm) cc_final: 0.7973 (mmt) REVERT: C 401 ASP cc_start: 0.6125 (p0) cc_final: 0.5539 (t0) REVERT: C 408 GLN cc_start: 0.7736 (mm110) cc_final: 0.7419 (mm-40) REVERT: C 411 TYR cc_start: 0.6261 (t80) cc_final: 0.5869 (t80) REVERT: C 415 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7125 (mt-10) REVERT: C 459 GLU cc_start: 0.8413 (pt0) cc_final: 0.7665 (mt-10) REVERT: C 483 PHE cc_start: 0.7224 (t80) cc_final: 0.6823 (t80) REVERT: D 101 MET cc_start: 0.6363 (mmt) cc_final: 0.5961 (tpp) REVERT: D 195 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5838 (mmp-170) REVERT: D 283 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6316 (mm-30) REVERT: D 287 MET cc_start: 0.5024 (ttp) cc_final: 0.3834 (tpt) REVERT: D 304 MET cc_start: 0.8020 (tpp) cc_final: 0.7691 (tpp) REVERT: D 308 LEU cc_start: 0.7958 (mt) cc_final: 0.7638 (mm) REVERT: D 343 LYS cc_start: 0.7875 (mtmm) cc_final: 0.6885 (tptm) REVERT: D 388 MET cc_start: 0.8254 (mmm) cc_final: 0.7973 (mmt) REVERT: D 401 ASP cc_start: 0.6122 (p0) cc_final: 0.5538 (t0) REVERT: D 408 GLN cc_start: 0.7735 (mm110) cc_final: 0.7418 (mm-40) REVERT: D 411 TYR cc_start: 0.6263 (t80) cc_final: 0.5842 (t80) REVERT: D 415 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7131 (mt-10) REVERT: D 459 GLU cc_start: 0.8407 (pt0) cc_final: 0.7654 (mt-10) REVERT: D 483 PHE cc_start: 0.7214 (t80) cc_final: 0.6810 (t80) outliers start: 8 outliers final: 8 residues processed: 327 average time/residue: 1.8038 time to fit residues: 648.0498 Evaluate side-chains 303 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 291 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 344 GLN A 355 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 421 HIS B 156 ASN B 344 GLN B 355 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 421 HIS C 156 ASN C 344 GLN C 355 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN C 421 HIS D 156 ASN D 344 GLN D 355 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN D 421 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123063 restraints weight = 14851.965| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.63 r_work: 0.3169 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15328 Z= 0.136 Angle : 0.552 6.459 20788 Z= 0.301 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.026 2596 Dihedral : 8.068 51.918 2236 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 7.68 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1920 helix: 1.37 (0.14), residues: 1300 sheet: -0.20 (0.49), residues: 112 loop : 0.47 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 281 HIS 0.005 0.001 HIS B 421 PHE 0.017 0.002 PHE B 569 TYR 0.014 0.002 TYR B 407 ARG 0.003 0.001 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 989) hydrogen bonds : angle 4.34060 ( 2871) covalent geometry : bond 0.00275 (15328) covalent geometry : angle 0.55158 (20788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6670 (mmp-170) REVERT: A 257 VAL cc_start: 0.7577 (t) cc_final: 0.7196 (p) REVERT: A 283 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6707 (tp30) REVERT: A 287 MET cc_start: 0.4353 (ttp) cc_final: 0.3368 (tpt) REVERT: A 304 MET cc_start: 0.8673 (tpp) cc_final: 0.8395 (tpp) REVERT: A 343 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7943 (tptm) REVERT: A 408 GLN cc_start: 0.8260 (mm110) cc_final: 0.8059 (mm-40) REVERT: A 411 TYR cc_start: 0.7165 (t80) cc_final: 0.6849 (t80) REVERT: A 422 LYS cc_start: 0.8712 (mttp) cc_final: 0.8493 (mttt) REVERT: A 433 ASP cc_start: 0.8236 (t70) cc_final: 0.7991 (m-30) REVERT: A 459 GLU cc_start: 0.8434 (pt0) cc_final: 0.7971 (mt-10) REVERT: A 483 PHE cc_start: 0.7119 (t80) cc_final: 0.6813 (t80) REVERT: B 101 MET cc_start: 0.6497 (mmt) cc_final: 0.6142 (tpp) REVERT: B 195 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6656 (mmp-170) REVERT: B 257 VAL cc_start: 0.7571 (t) cc_final: 0.7188 (p) REVERT: B 283 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6723 (tp30) REVERT: B 287 MET cc_start: 0.4362 (ttp) cc_final: 0.3405 (tpt) REVERT: B 304 MET cc_start: 0.8678 (tpp) cc_final: 0.8409 (tpp) REVERT: B 343 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7931 (tptm) REVERT: B 411 TYR cc_start: 0.7149 (t80) cc_final: 0.6840 (t80) REVERT: B 422 LYS cc_start: 0.8712 (mttp) cc_final: 0.8491 (mttt) REVERT: B 433 ASP cc_start: 0.8243 (t70) cc_final: 0.8002 (m-30) REVERT: B 459 GLU cc_start: 0.8434 (pt0) cc_final: 0.7974 (mt-10) REVERT: B 483 PHE cc_start: 0.7122 (t80) cc_final: 0.6817 (t80) REVERT: C 187 LEU cc_start: 0.7672 (tp) cc_final: 0.7455 (tt) REVERT: C 195 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6669 (mmp-170) REVERT: C 257 VAL cc_start: 0.7570 (t) cc_final: 0.7191 (p) REVERT: C 283 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6703 (tp30) REVERT: C 287 MET cc_start: 0.4367 (ttp) cc_final: 0.3403 (tpt) REVERT: C 304 MET cc_start: 0.8675 (tpp) cc_final: 0.8405 (tpp) REVERT: C 343 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7925 (tptm) REVERT: C 408 GLN cc_start: 0.8238 (mm110) cc_final: 0.8035 (mm-40) REVERT: C 411 TYR cc_start: 0.7165 (t80) cc_final: 0.6842 (t80) REVERT: C 422 LYS cc_start: 0.8700 (mttp) cc_final: 0.8479 (mttt) REVERT: C 433 ASP cc_start: 0.8240 (t70) cc_final: 0.8000 (m-30) REVERT: C 459 GLU cc_start: 0.8445 (pt0) cc_final: 0.7993 (mt-10) REVERT: C 483 PHE cc_start: 0.7107 (t80) cc_final: 0.6795 (t80) REVERT: D 195 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6664 (mmp-170) REVERT: D 257 VAL cc_start: 0.7568 (t) cc_final: 0.7183 (p) REVERT: D 283 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6703 (tp30) REVERT: D 287 MET cc_start: 0.4353 (ttp) cc_final: 0.3382 (tpt) REVERT: D 304 MET cc_start: 0.8670 (tpp) cc_final: 0.8401 (tpp) REVERT: D 343 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7889 (tptt) REVERT: D 408 GLN cc_start: 0.8242 (mm110) cc_final: 0.8037 (mm-40) REVERT: D 411 TYR cc_start: 0.7168 (t80) cc_final: 0.6844 (t80) REVERT: D 422 LYS cc_start: 0.8696 (mttp) cc_final: 0.8476 (mttt) REVERT: D 433 ASP cc_start: 0.8241 (t70) cc_final: 0.8003 (m-30) REVERT: D 459 GLU cc_start: 0.8448 (pt0) cc_final: 0.7995 (mt-10) REVERT: D 483 PHE cc_start: 0.7098 (t80) cc_final: 0.6787 (t80) outliers start: 28 outliers final: 4 residues processed: 308 average time/residue: 1.3154 time to fit residues: 444.5890 Evaluate side-chains 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120869 restraints weight = 14902.180| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.63 r_work: 0.3142 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15328 Z= 0.164 Angle : 0.560 6.364 20788 Z= 0.304 Chirality : 0.044 0.165 2348 Planarity : 0.004 0.028 2596 Dihedral : 7.962 55.078 2228 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.00 % Allowed : 8.52 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 1920 helix: 1.75 (0.14), residues: 1276 sheet: 0.61 (0.54), residues: 88 loop : 0.43 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 281 HIS 0.004 0.001 HIS D 437 PHE 0.017 0.002 PHE A 186 TYR 0.022 0.002 TYR D 347 ARG 0.003 0.001 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.05348 ( 989) hydrogen bonds : angle 4.22235 ( 2871) covalent geometry : bond 0.00375 (15328) covalent geometry : angle 0.56026 (20788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 1.651 Fit side-chains REVERT: A 208 LEU cc_start: 0.6718 (mt) cc_final: 0.6382 (mt) REVERT: A 257 VAL cc_start: 0.7548 (t) cc_final: 0.7170 (p) REVERT: A 283 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6732 (tp30) REVERT: A 287 MET cc_start: 0.4700 (ttp) cc_final: 0.3744 (tpt) REVERT: A 304 MET cc_start: 0.8666 (tpp) cc_final: 0.8465 (tpp) REVERT: A 343 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7907 (tptm) REVERT: A 433 ASP cc_start: 0.8317 (t70) cc_final: 0.7961 (m-30) REVERT: A 459 GLU cc_start: 0.8450 (pt0) cc_final: 0.7996 (mt-10) REVERT: A 483 PHE cc_start: 0.7078 (t80) cc_final: 0.6783 (t80) REVERT: B 208 LEU cc_start: 0.6722 (mt) cc_final: 0.6389 (mt) REVERT: B 257 VAL cc_start: 0.7548 (t) cc_final: 0.7164 (p) REVERT: B 283 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6728 (tp30) REVERT: B 287 MET cc_start: 0.4702 (ttp) cc_final: 0.3734 (tpt) REVERT: B 343 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7912 (tptm) REVERT: B 422 LYS cc_start: 0.8720 (mttp) cc_final: 0.8458 (mttt) REVERT: B 433 ASP cc_start: 0.8303 (t70) cc_final: 0.7954 (m-30) REVERT: B 459 GLU cc_start: 0.8449 (pt0) cc_final: 0.7997 (mt-10) REVERT: B 483 PHE cc_start: 0.7075 (t80) cc_final: 0.6772 (t80) REVERT: C 208 LEU cc_start: 0.6738 (mt) cc_final: 0.6406 (mt) REVERT: C 257 VAL cc_start: 0.7540 (t) cc_final: 0.7151 (p) REVERT: C 283 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6729 (tp30) REVERT: C 287 MET cc_start: 0.4718 (ttp) cc_final: 0.3752 (tpt) REVERT: C 343 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7911 (tptm) REVERT: C 433 ASP cc_start: 0.8307 (t70) cc_final: 0.7944 (m-30) REVERT: C 459 GLU cc_start: 0.8440 (pt0) cc_final: 0.7991 (mt-10) REVERT: C 483 PHE cc_start: 0.7069 (t80) cc_final: 0.6768 (t80) REVERT: D 208 LEU cc_start: 0.6732 (mt) cc_final: 0.6396 (mt) REVERT: D 257 VAL cc_start: 0.7554 (t) cc_final: 0.7168 (p) REVERT: D 283 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6714 (tp30) REVERT: D 287 MET cc_start: 0.4722 (ttp) cc_final: 0.3742 (tpt) REVERT: D 343 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7868 (tptt) REVERT: D 433 ASP cc_start: 0.8320 (t70) cc_final: 0.7956 (m-30) REVERT: D 459 GLU cc_start: 0.8436 (pt0) cc_final: 0.7991 (mt-10) REVERT: D 483 PHE cc_start: 0.7046 (t80) cc_final: 0.6755 (t80) outliers start: 43 outliers final: 19 residues processed: 305 average time/residue: 1.3434 time to fit residues: 448.9647 Evaluate side-chains 250 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 523 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 65 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 398 GLN C 398 GLN D 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.168114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120169 restraints weight = 14813.221| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.61 r_work: 0.3122 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15328 Z= 0.175 Angle : 0.558 6.580 20788 Z= 0.302 Chirality : 0.044 0.158 2348 Planarity : 0.004 0.034 2596 Dihedral : 7.534 52.631 2212 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.00 % Allowed : 9.85 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1920 helix: 1.79 (0.14), residues: 1280 sheet: 0.44 (0.54), residues: 88 loop : 0.21 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 281 HIS 0.004 0.001 HIS B 437 PHE 0.015 0.002 PHE C 186 TYR 0.022 0.002 TYR A 347 ARG 0.004 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.05360 ( 989) hydrogen bonds : angle 4.22732 ( 2871) covalent geometry : bond 0.00404 (15328) covalent geometry : angle 0.55825 (20788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.646 Fit side-chains REVERT: A 257 VAL cc_start: 0.7552 (t) cc_final: 0.7146 (p) REVERT: A 283 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6730 (tp30) REVERT: A 287 MET cc_start: 0.4607 (ttp) cc_final: 0.3528 (tpt) REVERT: A 343 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7894 (tptm) REVERT: A 433 ASP cc_start: 0.8314 (t70) cc_final: 0.7971 (m-30) REVERT: A 459 GLU cc_start: 0.8405 (pt0) cc_final: 0.7981 (mt-10) REVERT: A 483 PHE cc_start: 0.6972 (t80) cc_final: 0.6707 (t80) REVERT: B 257 VAL cc_start: 0.7555 (t) cc_final: 0.7148 (p) REVERT: B 283 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6732 (tp30) REVERT: B 287 MET cc_start: 0.4613 (ttp) cc_final: 0.3528 (tpt) REVERT: B 343 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7889 (tptm) REVERT: B 422 LYS cc_start: 0.8732 (mttp) cc_final: 0.8458 (mttt) REVERT: B 433 ASP cc_start: 0.8314 (t70) cc_final: 0.7967 (m-30) REVERT: B 459 GLU cc_start: 0.8410 (pt0) cc_final: 0.7989 (mt-10) REVERT: B 483 PHE cc_start: 0.6990 (t80) cc_final: 0.6729 (t80) REVERT: C 257 VAL cc_start: 0.7546 (t) cc_final: 0.7138 (p) REVERT: C 283 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6740 (tp30) REVERT: C 287 MET cc_start: 0.4605 (ttp) cc_final: 0.3534 (tpt) REVERT: C 343 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7885 (tptm) REVERT: C 433 ASP cc_start: 0.8331 (t70) cc_final: 0.7960 (m-30) REVERT: C 459 GLU cc_start: 0.8406 (pt0) cc_final: 0.7988 (mt-10) REVERT: C 483 PHE cc_start: 0.6980 (t80) cc_final: 0.6704 (t80) REVERT: D 257 VAL cc_start: 0.7556 (t) cc_final: 0.7148 (p) REVERT: D 283 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6730 (tp30) REVERT: D 287 MET cc_start: 0.4613 (ttp) cc_final: 0.3525 (tpt) REVERT: D 433 ASP cc_start: 0.8326 (t70) cc_final: 0.7958 (m-30) REVERT: D 459 GLU cc_start: 0.8412 (pt0) cc_final: 0.7992 (mt-10) REVERT: D 483 PHE cc_start: 0.6980 (t80) cc_final: 0.6716 (t80) outliers start: 43 outliers final: 22 residues processed: 285 average time/residue: 1.3144 time to fit residues: 410.8567 Evaluate side-chains 271 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 523 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120570 restraints weight = 15068.824| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.61 r_work: 0.3122 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15328 Z= 0.154 Angle : 0.532 6.298 20788 Z= 0.286 Chirality : 0.043 0.173 2348 Planarity : 0.003 0.023 2596 Dihedral : 7.267 54.258 2212 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.37 % Allowed : 12.01 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1920 helix: 1.94 (0.14), residues: 1280 sheet: 0.47 (0.54), residues: 88 loop : 0.15 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 281 HIS 0.004 0.001 HIS A 437 PHE 0.013 0.002 PHE B 389 TYR 0.023 0.002 TYR D 347 ARG 0.003 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 989) hydrogen bonds : angle 4.13352 ( 2871) covalent geometry : bond 0.00348 (15328) covalent geometry : angle 0.53204 (20788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 1.781 Fit side-chains REVERT: A 257 VAL cc_start: 0.7471 (t) cc_final: 0.7042 (p) REVERT: A 283 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6718 (tp30) REVERT: A 287 MET cc_start: 0.4542 (ttp) cc_final: 0.3608 (tpt) REVERT: A 343 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7894 (tptm) REVERT: A 433 ASP cc_start: 0.8288 (t70) cc_final: 0.7997 (m-30) REVERT: A 459 GLU cc_start: 0.8359 (pt0) cc_final: 0.7962 (mt-10) REVERT: A 473 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.6032 (tmm) REVERT: A 483 PHE cc_start: 0.6958 (t80) cc_final: 0.6681 (t80) REVERT: B 257 VAL cc_start: 0.7472 (t) cc_final: 0.7041 (p) REVERT: B 283 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6722 (tp30) REVERT: B 287 MET cc_start: 0.4552 (ttp) cc_final: 0.3608 (tpt) REVERT: B 343 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7889 (tptm) REVERT: B 422 LYS cc_start: 0.8722 (mttp) cc_final: 0.8466 (mttt) REVERT: B 433 ASP cc_start: 0.8289 (t70) cc_final: 0.7975 (m-30) REVERT: B 459 GLU cc_start: 0.8363 (pt0) cc_final: 0.7966 (mt-10) REVERT: B 483 PHE cc_start: 0.6975 (t80) cc_final: 0.6705 (t80) REVERT: C 257 VAL cc_start: 0.7455 (t) cc_final: 0.7026 (p) REVERT: C 283 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6731 (tp30) REVERT: C 287 MET cc_start: 0.4539 (ttp) cc_final: 0.3608 (tpt) REVERT: C 343 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7886 (tptm) REVERT: C 433 ASP cc_start: 0.8289 (t70) cc_final: 0.7979 (m-30) REVERT: C 459 GLU cc_start: 0.8354 (pt0) cc_final: 0.7962 (mt-10) REVERT: C 483 PHE cc_start: 0.6968 (t80) cc_final: 0.6700 (t80) REVERT: D 257 VAL cc_start: 0.7470 (t) cc_final: 0.7042 (p) REVERT: D 283 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6722 (tp30) REVERT: D 287 MET cc_start: 0.4551 (ttp) cc_final: 0.3595 (tpt) REVERT: D 433 ASP cc_start: 0.8290 (t70) cc_final: 0.7980 (m-30) REVERT: D 459 GLU cc_start: 0.8359 (pt0) cc_final: 0.7965 (mt-10) REVERT: D 483 PHE cc_start: 0.6961 (t80) cc_final: 0.6700 (t80) outliers start: 34 outliers final: 16 residues processed: 284 average time/residue: 1.2789 time to fit residues: 400.0091 Evaluate side-chains 247 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123120 restraints weight = 15031.495| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.62 r_work: 0.3175 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15328 Z= 0.112 Angle : 0.483 6.250 20788 Z= 0.256 Chirality : 0.041 0.178 2348 Planarity : 0.003 0.023 2596 Dihedral : 6.228 48.999 2212 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.68 % Allowed : 13.41 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 1920 helix: 2.15 (0.14), residues: 1288 sheet: 0.44 (0.52), residues: 88 loop : 0.36 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 281 HIS 0.003 0.001 HIS A 437 PHE 0.009 0.001 PHE A 389 TYR 0.019 0.001 TYR A 411 ARG 0.002 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 989) hydrogen bonds : angle 3.93737 ( 2871) covalent geometry : bond 0.00234 (15328) covalent geometry : angle 0.48270 (20788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 1.806 Fit side-chains REVERT: A 208 LEU cc_start: 0.6550 (mt) cc_final: 0.6292 (mt) REVERT: A 257 VAL cc_start: 0.7397 (t) cc_final: 0.6940 (p) REVERT: A 283 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6670 (tp30) REVERT: A 287 MET cc_start: 0.4301 (ttp) cc_final: 0.3248 (tpt) REVERT: A 343 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7883 (tptm) REVERT: A 429 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7893 (tp40) REVERT: A 459 GLU cc_start: 0.8326 (pt0) cc_final: 0.7959 (mt-10) REVERT: A 473 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6057 (tmm) REVERT: A 483 PHE cc_start: 0.6984 (t80) cc_final: 0.6706 (t80) REVERT: B 257 VAL cc_start: 0.7387 (t) cc_final: 0.6932 (p) REVERT: B 283 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6670 (tp30) REVERT: B 287 MET cc_start: 0.4315 (ttp) cc_final: 0.3237 (tpt) REVERT: B 343 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7885 (tptm) REVERT: B 429 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7875 (tp40) REVERT: B 433 ASP cc_start: 0.8247 (t70) cc_final: 0.8027 (m-30) REVERT: B 459 GLU cc_start: 0.8339 (pt0) cc_final: 0.7966 (mt-10) REVERT: B 473 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5312 (tmm) REVERT: B 483 PHE cc_start: 0.6994 (t80) cc_final: 0.6720 (t80) REVERT: C 208 LEU cc_start: 0.6567 (mt) cc_final: 0.6304 (mt) REVERT: C 257 VAL cc_start: 0.7363 (t) cc_final: 0.6908 (p) REVERT: C 283 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6671 (tp30) REVERT: C 287 MET cc_start: 0.4295 (ttp) cc_final: 0.3243 (tpt) REVERT: C 343 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7878 (tptm) REVERT: C 429 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7873 (tp40) REVERT: C 433 ASP cc_start: 0.8244 (t70) cc_final: 0.8020 (m-30) REVERT: C 459 GLU cc_start: 0.8340 (pt0) cc_final: 0.7968 (mt-10) REVERT: C 483 PHE cc_start: 0.6986 (t80) cc_final: 0.6718 (t80) REVERT: D 208 LEU cc_start: 0.6549 (mt) cc_final: 0.6286 (mt) REVERT: D 257 VAL cc_start: 0.7396 (t) cc_final: 0.6941 (p) REVERT: D 283 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6672 (tp30) REVERT: D 287 MET cc_start: 0.4301 (ttp) cc_final: 0.3252 (tpt) REVERT: D 429 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7881 (tp40) REVERT: D 433 ASP cc_start: 0.8257 (t70) cc_final: 0.8030 (m-30) REVERT: D 459 GLU cc_start: 0.8337 (pt0) cc_final: 0.7970 (mt-10) REVERT: D 483 PHE cc_start: 0.7003 (t80) cc_final: 0.6743 (t80) outliers start: 24 outliers final: 12 residues processed: 265 average time/residue: 1.2140 time to fit residues: 355.2494 Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118703 restraints weight = 15070.616| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.61 r_work: 0.3098 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15328 Z= 0.246 Angle : 0.635 7.288 20788 Z= 0.341 Chirality : 0.047 0.189 2348 Planarity : 0.004 0.028 2596 Dihedral : 7.997 58.310 2212 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.96 % Allowed : 12.36 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1920 helix: 1.84 (0.14), residues: 1280 sheet: 0.40 (0.54), residues: 88 loop : -0.09 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 281 HIS 0.005 0.002 HIS D 392 PHE 0.019 0.003 PHE C 186 TYR 0.032 0.003 TYR A 411 ARG 0.004 0.001 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 989) hydrogen bonds : angle 4.27391 ( 2871) covalent geometry : bond 0.00588 (15328) covalent geometry : angle 0.63550 (20788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 2.078 Fit side-chains REVERT: A 187 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 257 VAL cc_start: 0.7465 (t) cc_final: 0.7027 (p) REVERT: A 283 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6748 (tp30) REVERT: A 287 MET cc_start: 0.4788 (ttp) cc_final: 0.3830 (tpt) REVERT: A 343 LYS cc_start: 0.8415 (mtmm) cc_final: 0.7901 (tptm) REVERT: A 459 GLU cc_start: 0.8349 (pt0) cc_final: 0.8004 (mt-10) REVERT: B 187 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7307 (tt) REVERT: B 257 VAL cc_start: 0.7462 (t) cc_final: 0.7025 (p) REVERT: B 283 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6738 (tp30) REVERT: B 287 MET cc_start: 0.4788 (ttp) cc_final: 0.3829 (tpt) REVERT: B 343 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7906 (tptm) REVERT: B 433 ASP cc_start: 0.8349 (t70) cc_final: 0.7961 (m-30) REVERT: B 459 GLU cc_start: 0.8360 (pt0) cc_final: 0.8008 (mt-10) REVERT: B 473 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5358 (tmm) REVERT: B 483 PHE cc_start: 0.6925 (t80) cc_final: 0.6718 (t80) REVERT: C 257 VAL cc_start: 0.7468 (t) cc_final: 0.7031 (p) REVERT: C 283 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6757 (tp30) REVERT: C 287 MET cc_start: 0.4802 (ttp) cc_final: 0.3836 (tpt) REVERT: C 343 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7897 (tptm) REVERT: C 433 ASP cc_start: 0.8307 (t70) cc_final: 0.7937 (m-30) REVERT: C 459 GLU cc_start: 0.8353 (pt0) cc_final: 0.8008 (mt-10) REVERT: C 483 PHE cc_start: 0.6925 (t80) cc_final: 0.6689 (t80) REVERT: D 187 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7312 (tt) REVERT: D 257 VAL cc_start: 0.7476 (t) cc_final: 0.7038 (p) REVERT: D 283 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6760 (tp30) REVERT: D 287 MET cc_start: 0.4793 (ttp) cc_final: 0.3822 (tpt) REVERT: D 433 ASP cc_start: 0.8354 (t70) cc_final: 0.7958 (m-30) REVERT: D 459 GLU cc_start: 0.8358 (pt0) cc_final: 0.8014 (mt-10) REVERT: D 483 PHE cc_start: 0.6915 (t80) cc_final: 0.6688 (t80) outliers start: 28 outliers final: 18 residues processed: 264 average time/residue: 1.5097 time to fit residues: 438.7879 Evaluate side-chains 258 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 485 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121905 restraints weight = 15001.915| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.61 r_work: 0.3139 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15328 Z= 0.122 Angle : 0.507 7.050 20788 Z= 0.269 Chirality : 0.041 0.191 2348 Planarity : 0.003 0.023 2596 Dihedral : 6.773 56.573 2212 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.54 % Allowed : 13.62 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 1920 helix: 2.12 (0.14), residues: 1284 sheet: 0.24 (0.53), residues: 88 loop : 0.11 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 281 HIS 0.003 0.001 HIS D 437 PHE 0.011 0.001 PHE A 389 TYR 0.021 0.002 TYR A 411 ARG 0.002 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 989) hydrogen bonds : angle 4.00842 ( 2871) covalent geometry : bond 0.00258 (15328) covalent geometry : angle 0.50743 (20788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.699 Fit side-chains REVERT: A 257 VAL cc_start: 0.7350 (t) cc_final: 0.6891 (p) REVERT: A 283 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6669 (tp30) REVERT: A 287 MET cc_start: 0.4370 (ttp) cc_final: 0.3358 (tpt) REVERT: A 343 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7884 (tptm) REVERT: A 459 GLU cc_start: 0.8350 (pt0) cc_final: 0.8001 (mt-10) REVERT: B 257 VAL cc_start: 0.7340 (t) cc_final: 0.6883 (p) REVERT: B 283 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6663 (tp30) REVERT: B 287 MET cc_start: 0.4381 (ttp) cc_final: 0.3339 (tpt) REVERT: B 343 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7886 (tptm) REVERT: B 433 ASP cc_start: 0.8261 (t70) cc_final: 0.8028 (m-30) REVERT: B 459 GLU cc_start: 0.8356 (pt0) cc_final: 0.8002 (mt-10) REVERT: B 473 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5346 (tmm) REVERT: C 257 VAL cc_start: 0.7339 (t) cc_final: 0.6884 (p) REVERT: C 283 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6677 (tp30) REVERT: C 287 MET cc_start: 0.4373 (ttp) cc_final: 0.3347 (tpt) REVERT: C 343 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7883 (tptm) REVERT: C 433 ASP cc_start: 0.8204 (t70) cc_final: 0.7999 (m-30) REVERT: C 459 GLU cc_start: 0.8353 (pt0) cc_final: 0.8002 (mt-10) REVERT: C 483 PHE cc_start: 0.6947 (t80) cc_final: 0.6739 (t80) REVERT: D 257 VAL cc_start: 0.7353 (t) cc_final: 0.6896 (p) REVERT: D 283 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6682 (tp30) REVERT: D 287 MET cc_start: 0.4375 (ttp) cc_final: 0.3347 (tpt) REVERT: D 433 ASP cc_start: 0.8261 (t70) cc_final: 0.8016 (m-30) REVERT: D 459 GLU cc_start: 0.8361 (pt0) cc_final: 0.8004 (mt-10) REVERT: D 483 PHE cc_start: 0.6948 (t80) cc_final: 0.6738 (t80) outliers start: 22 outliers final: 9 residues processed: 256 average time/residue: 1.5151 time to fit residues: 429.2543 Evaluate side-chains 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 24 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122767 restraints weight = 15012.775| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15328 Z= 0.112 Angle : 0.490 7.753 20788 Z= 0.258 Chirality : 0.041 0.188 2348 Planarity : 0.003 0.024 2596 Dihedral : 6.137 52.653 2212 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 1920 helix: 2.25 (0.14), residues: 1288 sheet: 0.20 (0.52), residues: 88 loop : 0.33 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 373 HIS 0.003 0.001 HIS B 437 PHE 0.009 0.001 PHE A 389 TYR 0.022 0.002 TYR D 411 ARG 0.002 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 989) hydrogen bonds : angle 3.88372 ( 2871) covalent geometry : bond 0.00232 (15328) covalent geometry : angle 0.49006 (20788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 1.639 Fit side-chains REVERT: A 257 VAL cc_start: 0.7323 (t) cc_final: 0.6855 (p) REVERT: A 283 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6510 (tp30) REVERT: A 287 MET cc_start: 0.4291 (ttp) cc_final: 0.3250 (tpt) REVERT: A 343 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7876 (tptm) REVERT: A 459 GLU cc_start: 0.8331 (pt0) cc_final: 0.7999 (mt-10) REVERT: B 208 LEU cc_start: 0.6533 (mt) cc_final: 0.6191 (mt) REVERT: B 257 VAL cc_start: 0.7307 (t) cc_final: 0.6843 (p) REVERT: B 283 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6517 (tp30) REVERT: B 287 MET cc_start: 0.4312 (ttp) cc_final: 0.3234 (tpt) REVERT: B 343 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7880 (tptm) REVERT: B 433 ASP cc_start: 0.8229 (t70) cc_final: 0.8013 (m-30) REVERT: B 459 GLU cc_start: 0.8335 (pt0) cc_final: 0.7997 (mt-10) REVERT: B 473 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5271 (tmm) REVERT: C 257 VAL cc_start: 0.7311 (t) cc_final: 0.6844 (p) REVERT: C 283 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6517 (tp30) REVERT: C 287 MET cc_start: 0.4308 (ttp) cc_final: 0.3256 (tpt) REVERT: C 343 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7876 (tptm) REVERT: C 459 GLU cc_start: 0.8335 (pt0) cc_final: 0.8004 (mt-10) REVERT: D 257 VAL cc_start: 0.7324 (t) cc_final: 0.6858 (p) REVERT: D 283 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6518 (tp30) REVERT: D 287 MET cc_start: 0.4304 (ttp) cc_final: 0.3244 (tpt) REVERT: D 433 ASP cc_start: 0.8244 (t70) cc_final: 0.8013 (m-30) REVERT: D 459 GLU cc_start: 0.8340 (pt0) cc_final: 0.8004 (mt-10) outliers start: 20 outliers final: 14 residues processed: 249 average time/residue: 1.2635 time to fit residues: 347.7167 Evaluate side-chains 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.0050 chunk 105 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124714 restraints weight = 15162.443| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.62 r_work: 0.3185 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.103 Angle : 0.481 8.683 20788 Z= 0.250 Chirality : 0.040 0.195 2348 Planarity : 0.003 0.024 2596 Dihedral : 5.607 49.265 2212 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.33 % Allowed : 14.53 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.19), residues: 1920 helix: 2.38 (0.14), residues: 1288 sheet: 0.21 (0.52), residues: 88 loop : 0.40 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 373 HIS 0.004 0.001 HIS D 437 PHE 0.009 0.001 PHE B 514 TYR 0.018 0.001 TYR D 411 ARG 0.002 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 989) hydrogen bonds : angle 3.77885 ( 2871) covalent geometry : bond 0.00207 (15328) covalent geometry : angle 0.48088 (20788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 1.502 Fit side-chains REVERT: A 218 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7401 (mt) REVERT: A 257 VAL cc_start: 0.7260 (t) cc_final: 0.6800 (p) REVERT: A 265 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 283 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6521 (tp30) REVERT: A 285 PHE cc_start: 0.6679 (m-10) cc_final: 0.6427 (m-80) REVERT: A 287 MET cc_start: 0.4070 (ttp) cc_final: 0.3121 (tpt) REVERT: A 343 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7851 (tptm) REVERT: A 459 GLU cc_start: 0.8327 (pt0) cc_final: 0.7983 (mt-10) REVERT: B 218 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7412 (mt) REVERT: B 257 VAL cc_start: 0.7246 (t) cc_final: 0.6783 (p) REVERT: B 283 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6523 (tp30) REVERT: B 285 PHE cc_start: 0.6687 (m-10) cc_final: 0.6429 (m-80) REVERT: B 287 MET cc_start: 0.4089 (ttp) cc_final: 0.3121 (tpt) REVERT: B 343 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7860 (tptm) REVERT: B 433 ASP cc_start: 0.8201 (t70) cc_final: 0.7960 (m-30) REVERT: B 459 GLU cc_start: 0.8336 (pt0) cc_final: 0.7987 (mt-10) REVERT: B 473 MET cc_start: 0.5718 (ttt) cc_final: 0.5123 (tmm) REVERT: C 218 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7393 (mt) REVERT: C 257 VAL cc_start: 0.7251 (t) cc_final: 0.6786 (p) REVERT: C 265 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7905 (mm) REVERT: C 283 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6521 (tp30) REVERT: C 285 PHE cc_start: 0.6687 (m-10) cc_final: 0.6435 (m-80) REVERT: C 287 MET cc_start: 0.4080 (ttp) cc_final: 0.3123 (tpt) REVERT: C 343 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7857 (tptm) REVERT: C 429 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7849 (tp40) REVERT: C 459 GLU cc_start: 0.8334 (pt0) cc_final: 0.7989 (mt-10) REVERT: D 218 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 257 VAL cc_start: 0.7271 (t) cc_final: 0.6806 (p) REVERT: D 283 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6531 (tp30) REVERT: D 285 PHE cc_start: 0.6679 (m-10) cc_final: 0.6427 (m-80) REVERT: D 287 MET cc_start: 0.4078 (ttp) cc_final: 0.3122 (tpt) REVERT: D 429 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7895 (tp40) REVERT: D 459 GLU cc_start: 0.8330 (pt0) cc_final: 0.7983 (mt-10) outliers start: 19 outliers final: 5 residues processed: 256 average time/residue: 1.2362 time to fit residues: 348.7106 Evaluate side-chains 247 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 103 optimal weight: 0.0470 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.170831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123476 restraints weight = 15117.706| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.61 r_work: 0.3159 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15328 Z= 0.115 Angle : 0.498 9.024 20788 Z= 0.260 Chirality : 0.041 0.189 2348 Planarity : 0.003 0.023 2596 Dihedral : 5.802 51.585 2212 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.77 % Allowed : 15.50 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 1920 helix: 2.41 (0.14), residues: 1288 sheet: 0.26 (0.52), residues: 88 loop : 0.37 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 373 HIS 0.004 0.001 HIS B 437 PHE 0.011 0.001 PHE B 483 TYR 0.021 0.002 TYR B 411 ARG 0.004 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 989) hydrogen bonds : angle 3.81236 ( 2871) covalent geometry : bond 0.00245 (15328) covalent geometry : angle 0.49761 (20788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15433.48 seconds wall clock time: 267 minutes 41.55 seconds (16061.55 seconds total)