Starting phenix.real_space_refine on Mon Jan 20 07:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc6_44425/01_2025/9bc6_44425.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc6_44425/01_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_44425/01_2025/9bc6_44425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc6_44425/01_2025/9bc6_44425.map" model { file = "/net/cci-nas-00/data/ceres_data/9bc6_44425/01_2025/9bc6_44425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc6_44425/01_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-5571/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: 9.19, per 1000 atoms: 0.61 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: 3.60 Conformation dependent library (CDL) restraints added in 2.2 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: 1.40 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: 4.65 Time building geometry restraints manager: 4.13 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: 0.03 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.080 Find NCS groups from input model: 0.780 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.130 ------------------------------------------------------------------------------- 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= 0.753 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 *********************** 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 : 1.597 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: 1.3674 time to fit residues: 490.0206 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 : 1.725 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123100 restraints weight = 14851.966| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.63 r_work: 0.3173 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- 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= 0.179 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 *********************** 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 : 1.647 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: 0.7581 (t) cc_final: 0.7200 (p) REVERT: A 283 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6713 (tp30) REVERT: A 287 MET cc_start: 0.4360 (ttp) cc_final: 0.3374 (tpt) REVERT: A 304 MET cc_start: 0.8674 (tpp) cc_final: 0.8395 (tpp) REVERT: A 343 LYS cc_start: 0.8435 (mtmm) cc_final: 0.7943 (tptm) REVERT: A 408 GLN cc_start: 0.8261 (mm110) cc_final: 0.8059 (mm-40) REVERT: A 411 TYR cc_start: 0.7160 (t80) cc_final: 0.6844 (t80) REVERT: A 422 LYS cc_start: 0.8713 (mttp) cc_final: 0.8494 (mttt) REVERT: A 433 ASP cc_start: 0.8237 (t70) cc_final: 0.7992 (m-30) REVERT: A 459 GLU cc_start: 0.8429 (pt0) cc_final: 0.7971 (mt-10) REVERT: A 483 PHE cc_start: 0.7118 (t80) cc_final: 0.6810 (t80) REVERT: B 101 MET cc_start: 0.6489 (mmt) cc_final: 0.6134 (tpp) REVERT: B 195 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6655 (mmp-170) REVERT: B 257 VAL cc_start: 0.7578 (t) cc_final: 0.7196 (p) REVERT: B 283 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6729 (tp30) REVERT: B 287 MET cc_start: 0.4369 (ttp) cc_final: 0.3411 (tpt) REVERT: B 304 MET cc_start: 0.8678 (tpp) cc_final: 0.8409 (tpp) REVERT: B 343 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7932 (tptm) REVERT: B 411 TYR cc_start: 0.7144 (t80) cc_final: 0.6836 (t80) REVERT: B 422 LYS cc_start: 0.8713 (mttp) cc_final: 0.8493 (mttt) REVERT: B 433 ASP cc_start: 0.8243 (t70) cc_final: 0.8002 (m-30) REVERT: B 459 GLU cc_start: 0.8428 (pt0) cc_final: 0.7973 (mt-10) REVERT: B 483 PHE cc_start: 0.7120 (t80) cc_final: 0.6815 (t80) REVERT: C 187 LEU cc_start: 0.7674 (tp) cc_final: 0.7456 (tt) REVERT: C 195 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6668 (mmp-170) REVERT: C 257 VAL cc_start: 0.7574 (t) cc_final: 0.7196 (p) REVERT: C 283 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6709 (tp30) REVERT: C 287 MET cc_start: 0.4373 (ttp) cc_final: 0.3410 (tpt) REVERT: C 304 MET cc_start: 0.8677 (tpp) cc_final: 0.8408 (tpp) REVERT: C 343 LYS cc_start: 0.8431 (mtmm) cc_final: 0.7926 (tptm) REVERT: C 408 GLN cc_start: 0.8238 (mm110) cc_final: 0.8035 (mm-40) REVERT: C 411 TYR cc_start: 0.7159 (t80) cc_final: 0.6836 (t80) REVERT: C 422 LYS cc_start: 0.8700 (mttp) cc_final: 0.8480 (mttt) REVERT: C 433 ASP cc_start: 0.8240 (t70) cc_final: 0.7999 (m-30) REVERT: C 459 GLU cc_start: 0.8441 (pt0) cc_final: 0.7994 (mt-10) REVERT: C 483 PHE cc_start: 0.7105 (t80) cc_final: 0.6793 (t80) REVERT: D 195 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6664 (mmp-170) REVERT: D 257 VAL cc_start: 0.7573 (t) cc_final: 0.7189 (p) REVERT: D 283 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6709 (tp30) REVERT: D 287 MET cc_start: 0.4359 (ttp) cc_final: 0.3388 (tpt) REVERT: D 304 MET cc_start: 0.8670 (tpp) cc_final: 0.8401 (tpp) REVERT: D 343 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7888 (tptt) REVERT: D 408 GLN cc_start: 0.8242 (mm110) cc_final: 0.8037 (mm-40) REVERT: D 411 TYR cc_start: 0.7164 (t80) cc_final: 0.6840 (t80) REVERT: D 422 LYS cc_start: 0.8698 (mttp) cc_final: 0.8478 (mttt) REVERT: D 433 ASP cc_start: 0.8240 (t70) cc_final: 0.8002 (m-30) REVERT: D 459 GLU cc_start: 0.8443 (pt0) cc_final: 0.7995 (mt-10) REVERT: D 483 PHE cc_start: 0.7096 (t80) cc_final: 0.6785 (t80) outliers start: 28 outliers final: 4 residues processed: 308 average time/residue: 1.2941 time to fit residues: 438.6559 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 : 1.588 ------------------------------------------------------------------------------- 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: 3.9990 chunk 131 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.169692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121855 restraints weight = 14909.336| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.62 r_work: 0.3143 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15328 Z= 0.213 Angle : 0.529 5.986 20788 Z= 0.287 Chirality : 0.043 0.162 2348 Planarity : 0.004 0.023 2596 Dihedral : 7.700 53.978 2228 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.72 % Allowed : 8.03 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1920 helix: 1.81 (0.14), residues: 1276 sheet: 0.60 (0.54), residues: 88 loop : 0.53 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 281 HIS 0.003 0.001 HIS C 437 PHE 0.015 0.002 PHE B 514 TYR 0.016 0.002 TYR B 407 ARG 0.003 0.000 ARG B 504 *********************** 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 328 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 1.736 Fit side-chains REVERT: A 195 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6710 (mmp-170) REVERT: A 208 LEU cc_start: 0.6710 (mt) cc_final: 0.6371 (mt) REVERT: A 257 VAL cc_start: 0.7530 (t) cc_final: 0.7148 (p) REVERT: A 283 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6712 (tp30) REVERT: A 287 MET cc_start: 0.4627 (ttp) cc_final: 0.3664 (tpt) REVERT: A 304 MET cc_start: 0.8675 (tpp) cc_final: 0.8468 (tpp) REVERT: A 343 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7923 (tptm) REVERT: A 408 GLN cc_start: 0.8254 (mm110) cc_final: 0.8054 (mm-40) REVERT: A 422 LYS cc_start: 0.8711 (mttp) cc_final: 0.8454 (mttt) REVERT: A 433 ASP cc_start: 0.8284 (t70) cc_final: 0.7963 (m-30) REVERT: A 459 GLU cc_start: 0.8449 (pt0) cc_final: 0.7987 (mt-10) REVERT: A 483 PHE cc_start: 0.7111 (t80) cc_final: 0.6826 (t80) REVERT: B 195 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6715 (mmp-170) REVERT: B 208 LEU cc_start: 0.6727 (mt) cc_final: 0.6392 (mt) REVERT: B 257 VAL cc_start: 0.7512 (t) cc_final: 0.7128 (p) REVERT: B 283 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6700 (tp30) REVERT: B 287 MET cc_start: 0.4629 (ttp) cc_final: 0.3653 (tpt) REVERT: B 304 MET cc_start: 0.8676 (tpp) cc_final: 0.8469 (tpp) REVERT: B 343 LYS cc_start: 0.8369 (mtmm) cc_final: 0.7923 (tptm) REVERT: B 422 LYS cc_start: 0.8709 (mttp) cc_final: 0.8449 (mttt) REVERT: B 433 ASP cc_start: 0.8284 (t70) cc_final: 0.7966 (m-30) REVERT: B 459 GLU cc_start: 0.8447 (pt0) cc_final: 0.7989 (mt-10) REVERT: B 483 PHE cc_start: 0.7122 (t80) cc_final: 0.6832 (t80) REVERT: C 195 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6715 (mmp-170) REVERT: C 208 LEU cc_start: 0.6730 (mt) cc_final: 0.6393 (mt) REVERT: C 257 VAL cc_start: 0.7518 (t) cc_final: 0.7129 (p) REVERT: C 283 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6687 (tp30) REVERT: C 287 MET cc_start: 0.4651 (ttp) cc_final: 0.3673 (tpt) REVERT: C 304 MET cc_start: 0.8677 (tpp) cc_final: 0.8469 (tpp) REVERT: C 343 LYS cc_start: 0.8369 (mtmm) cc_final: 0.7920 (tptm) REVERT: C 408 GLN cc_start: 0.8258 (mm110) cc_final: 0.8057 (mm-40) REVERT: C 422 LYS cc_start: 0.8704 (mttp) cc_final: 0.8443 (mttt) REVERT: C 433 ASP cc_start: 0.8302 (t70) cc_final: 0.7974 (m-30) REVERT: C 459 GLU cc_start: 0.8443 (pt0) cc_final: 0.7986 (mt-10) REVERT: C 483 PHE cc_start: 0.7108 (t80) cc_final: 0.6807 (t80) REVERT: D 195 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6708 (mmp-170) REVERT: D 208 LEU cc_start: 0.6716 (mt) cc_final: 0.6377 (mt) REVERT: D 257 VAL cc_start: 0.7533 (t) cc_final: 0.7147 (p) REVERT: D 283 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6677 (tp30) REVERT: D 287 MET cc_start: 0.4651 (ttp) cc_final: 0.3666 (tpt) REVERT: D 304 MET cc_start: 0.8677 (tpp) cc_final: 0.8472 (tpp) REVERT: D 343 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7882 (tptt) REVERT: D 422 LYS cc_start: 0.8706 (mttp) cc_final: 0.8445 (mttt) REVERT: D 433 ASP cc_start: 0.8304 (t70) cc_final: 0.7978 (m-30) REVERT: D 459 GLU cc_start: 0.8438 (pt0) cc_final: 0.7987 (mt-10) REVERT: D 483 PHE cc_start: 0.7088 (t80) cc_final: 0.6800 (t80) outliers start: 39 outliers final: 19 residues processed: 309 average time/residue: 1.3020 time to fit residues: 441.8970 Evaluate side-chains 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 195 ARG 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 195 ARG 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 195 ARG 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 195 ARG 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: 0.7980 chunk 139 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.169386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121472 restraints weight = 14837.029| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15328 Z= 0.213 Angle : 0.517 6.100 20788 Z= 0.279 Chirality : 0.042 0.160 2348 Planarity : 0.004 0.029 2596 Dihedral : 7.488 55.649 2228 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 9.85 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.19), residues: 1920 helix: 1.94 (0.14), residues: 1272 sheet: 0.40 (0.51), residues: 88 loop : 0.38 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 281 HIS 0.004 0.001 HIS D 437 PHE 0.013 0.002 PHE C 186 TYR 0.022 0.002 TYR A 347 ARG 0.003 0.000 ARG A 126 *********************** 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 299 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 1.596 Fit side-chains REVERT: A 195 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6686 (mmp-170) REVERT: A 257 VAL cc_start: 0.7527 (t) cc_final: 0.7120 (p) REVERT: A 283 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6705 (tp30) REVERT: A 287 MET cc_start: 0.4572 (ttp) cc_final: 0.3588 (tpt) REVERT: A 343 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7898 (tptm) REVERT: A 408 GLN cc_start: 0.8260 (mm110) cc_final: 0.8047 (mm-40) REVERT: A 422 LYS cc_start: 0.8701 (mttp) cc_final: 0.8434 (mttt) REVERT: A 433 ASP cc_start: 0.8288 (t70) cc_final: 0.7966 (m-30) REVERT: A 459 GLU cc_start: 0.8383 (pt0) cc_final: 0.7956 (mt-10) REVERT: A 483 PHE cc_start: 0.7028 (t80) cc_final: 0.6753 (t80) REVERT: B 195 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6694 (mmp-170) REVERT: B 257 VAL cc_start: 0.7523 (t) cc_final: 0.7119 (p) REVERT: B 283 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6680 (tp30) REVERT: B 287 MET cc_start: 0.4563 (ttp) cc_final: 0.3565 (tpt) REVERT: B 343 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7905 (tptm) REVERT: B 422 LYS cc_start: 0.8701 (mttp) cc_final: 0.8433 (mttt) REVERT: B 433 ASP cc_start: 0.8286 (t70) cc_final: 0.7966 (m-30) REVERT: B 459 GLU cc_start: 0.8391 (pt0) cc_final: 0.7961 (mt-10) REVERT: B 483 PHE cc_start: 0.7027 (t80) cc_final: 0.6747 (t80) REVERT: C 195 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6703 (mmp-170) REVERT: C 257 VAL cc_start: 0.7515 (t) cc_final: 0.7107 (p) REVERT: C 283 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6713 (tp30) REVERT: C 287 MET cc_start: 0.4564 (ttp) cc_final: 0.3579 (tpt) REVERT: C 343 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7901 (tptm) REVERT: C 408 GLN cc_start: 0.8257 (mm110) cc_final: 0.8048 (mm-40) REVERT: C 422 LYS cc_start: 0.8697 (mttp) cc_final: 0.8430 (mttt) REVERT: C 433 ASP cc_start: 0.8301 (t70) cc_final: 0.7966 (m-30) REVERT: C 459 GLU cc_start: 0.8402 (pt0) cc_final: 0.7972 (mt-10) REVERT: C 483 PHE cc_start: 0.7022 (t80) cc_final: 0.6732 (t80) REVERT: D 195 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6692 (mmp-170) REVERT: D 257 VAL cc_start: 0.7532 (t) cc_final: 0.7124 (p) REVERT: D 283 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6704 (tp30) REVERT: D 287 MET cc_start: 0.4571 (ttp) cc_final: 0.3572 (tpt) REVERT: D 343 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7851 (tptt) REVERT: D 422 LYS cc_start: 0.8698 (mttp) cc_final: 0.8431 (mttt) REVERT: D 433 ASP cc_start: 0.8301 (t70) cc_final: 0.7966 (m-30) REVERT: D 459 GLU cc_start: 0.8387 (pt0) cc_final: 0.7959 (mt-10) REVERT: D 483 PHE cc_start: 0.7018 (t80) cc_final: 0.6737 (t80) outliers start: 38 outliers final: 10 residues processed: 283 average time/residue: 1.4024 time to fit residues: 434.6555 Evaluate side-chains 266 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 298 ILE 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: 3.9990 chunk 38 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120066 restraints weight = 15048.655| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.63 r_work: 0.3121 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15328 Z= 0.286 Angle : 0.568 6.780 20788 Z= 0.306 Chirality : 0.044 0.171 2348 Planarity : 0.004 0.030 2596 Dihedral : 8.147 55.718 2228 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.30 % Allowed : 12.08 % 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: 1.95 (0.19), residues: 1920 helix: 1.86 (0.14), residues: 1280 sheet: 0.37 (0.53), residues: 88 loop : 0.22 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 281 HIS 0.004 0.001 HIS C 392 PHE 0.017 0.002 PHE A 186 TYR 0.023 0.003 TYR D 347 ARG 0.004 0.001 ARG B 126 *********************** 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 298 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 1.581 Fit side-chains REVERT: A 257 VAL cc_start: 0.7545 (t) cc_final: 0.7122 (p) REVERT: A 283 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6740 (tp30) REVERT: A 287 MET cc_start: 0.4726 (ttp) cc_final: 0.3625 (tpt) REVERT: A 343 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7909 (tptm) REVERT: A 408 GLN cc_start: 0.8268 (mm110) cc_final: 0.8041 (mm-40) REVERT: A 422 LYS cc_start: 0.8743 (mttp) cc_final: 0.8465 (mttt) REVERT: A 433 ASP cc_start: 0.8305 (t70) cc_final: 0.7952 (m-30) REVERT: A 459 GLU cc_start: 0.8385 (pt0) cc_final: 0.7975 (mt-10) REVERT: A 483 PHE cc_start: 0.6960 (t80) cc_final: 0.6698 (t80) REVERT: B 257 VAL cc_start: 0.7534 (t) cc_final: 0.7109 (p) REVERT: B 283 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6757 (tp30) REVERT: B 287 MET cc_start: 0.4696 (ttp) cc_final: 0.3578 (tpt) REVERT: B 343 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7903 (tptm) REVERT: B 422 LYS cc_start: 0.8745 (mttp) cc_final: 0.8469 (mttt) REVERT: B 433 ASP cc_start: 0.8310 (t70) cc_final: 0.7970 (m-30) REVERT: B 459 GLU cc_start: 0.8389 (pt0) cc_final: 0.7985 (mt-10) REVERT: B 473 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5294 (tmm) REVERT: B 483 PHE cc_start: 0.6954 (t80) cc_final: 0.6692 (t80) REVERT: C 257 VAL cc_start: 0.7534 (t) cc_final: 0.7106 (p) REVERT: C 283 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6745 (tp30) REVERT: C 287 MET cc_start: 0.4708 (ttp) cc_final: 0.3609 (tpt) REVERT: C 343 LYS cc_start: 0.8400 (mtmm) cc_final: 0.7901 (tptm) REVERT: C 408 GLN cc_start: 0.8263 (mm110) cc_final: 0.8037 (mm-40) REVERT: C 422 LYS cc_start: 0.8734 (mttp) cc_final: 0.8454 (mttt) REVERT: C 433 ASP cc_start: 0.8327 (t70) cc_final: 0.7963 (m-30) REVERT: C 459 GLU cc_start: 0.8381 (pt0) cc_final: 0.7981 (mt-10) REVERT: C 483 PHE cc_start: 0.6939 (t80) cc_final: 0.6671 (t80) REVERT: D 257 VAL cc_start: 0.7544 (t) cc_final: 0.7119 (p) REVERT: D 283 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6751 (tp30) REVERT: D 287 MET cc_start: 0.4730 (ttp) cc_final: 0.3608 (tpt) REVERT: D 422 LYS cc_start: 0.8730 (mttp) cc_final: 0.8451 (mttt) REVERT: D 433 ASP cc_start: 0.8330 (t70) cc_final: 0.7963 (m-30) REVERT: D 459 GLU cc_start: 0.8368 (pt0) cc_final: 0.7970 (mt-10) REVERT: D 483 PHE cc_start: 0.6931 (t80) cc_final: 0.6671 (t80) outliers start: 33 outliers final: 18 residues processed: 289 average time/residue: 1.3290 time to fit residues: 420.8647 Evaluate side-chains 272 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 485 THR 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 B residue 485 THR 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 C residue 523 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 158 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.170927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123316 restraints weight = 14993.889| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.62 r_work: 0.3158 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2643 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= 0.151 Angle : 0.475 5.385 20788 Z= 0.254 Chirality : 0.040 0.178 2348 Planarity : 0.003 0.022 2596 Dihedral : 6.335 48.407 2212 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.82 % Allowed : 12.71 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.19), residues: 1920 helix: 2.10 (0.14), residues: 1288 sheet: 0.32 (0.52), residues: 88 loop : 0.50 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 281 HIS 0.003 0.001 HIS C 437 PHE 0.009 0.001 PHE C 389 TYR 0.018 0.001 TYR D 347 ARG 0.002 0.000 ARG D 504 *********************** 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 280 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 1.758 Fit side-chains REVERT: A 257 VAL cc_start: 0.7400 (t) cc_final: 0.6954 (p) REVERT: A 283 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6691 (tp30) REVERT: A 287 MET cc_start: 0.4270 (ttp) cc_final: 0.3311 (tpt) REVERT: A 343 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7882 (tptm) REVERT: A 408 GLN cc_start: 0.8267 (mm110) cc_final: 0.8050 (mm-40) REVERT: A 433 ASP cc_start: 0.8236 (t70) cc_final: 0.7991 (m-30) REVERT: A 459 GLU cc_start: 0.8354 (pt0) cc_final: 0.7967 (mt-10) REVERT: A 483 PHE cc_start: 0.6995 (t80) cc_final: 0.6722 (t80) REVERT: B 257 VAL cc_start: 0.7390 (t) cc_final: 0.6942 (p) REVERT: B 283 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6675 (tp30) REVERT: B 287 MET cc_start: 0.4267 (ttp) cc_final: 0.3281 (tpt) REVERT: B 343 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7883 (tptm) REVERT: B 429 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7869 (tp40) REVERT: B 433 ASP cc_start: 0.8247 (t70) cc_final: 0.8020 (m-30) REVERT: B 459 GLU cc_start: 0.8358 (pt0) cc_final: 0.7969 (mt-10) REVERT: B 473 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.5221 (tmm) REVERT: B 483 PHE cc_start: 0.6977 (t80) cc_final: 0.6707 (t80) REVERT: C 257 VAL cc_start: 0.7393 (t) cc_final: 0.6940 (p) REVERT: C 283 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6685 (tp30) REVERT: C 287 MET cc_start: 0.4272 (ttp) cc_final: 0.3311 (tpt) REVERT: C 343 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7882 (tptm) REVERT: C 408 GLN cc_start: 0.8265 (mm110) cc_final: 0.8049 (mm-40) REVERT: C 429 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7877 (tp40) REVERT: C 433 ASP cc_start: 0.8241 (t70) cc_final: 0.8015 (m-30) REVERT: C 459 GLU cc_start: 0.8357 (pt0) cc_final: 0.7976 (mt-10) REVERT: C 483 PHE cc_start: 0.6974 (t80) cc_final: 0.6699 (t80) REVERT: D 257 VAL cc_start: 0.7402 (t) cc_final: 0.6953 (p) REVERT: D 283 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6674 (tp30) REVERT: D 287 MET cc_start: 0.4286 (ttp) cc_final: 0.3307 (tpt) REVERT: D 343 LYS cc_start: 0.8495 (mtpp) cc_final: 0.7908 (tptt) REVERT: D 429 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7862 (tp40) REVERT: D 433 ASP cc_start: 0.8241 (t70) cc_final: 0.8009 (m-30) REVERT: D 459 GLU cc_start: 0.8349 (pt0) cc_final: 0.7967 (mt-10) REVERT: D 483 PHE cc_start: 0.6975 (t80) cc_final: 0.6703 (t80) outliers start: 26 outliers final: 11 residues processed: 273 average time/residue: 1.2772 time to fit residues: 383.4395 Evaluate side-chains 248 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 370 SER Chi-restraints excluded: chain B residue 473 MET 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: 4.9990 chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 156 ASN B 355 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118258 restraints weight = 15050.193| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.61 r_work: 0.3123 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15328 Z= 0.443 Angle : 0.681 7.846 20788 Z= 0.365 Chirality : 0.048 0.192 2348 Planarity : 0.005 0.032 2596 Dihedral : 8.423 58.357 2212 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 12.64 % Favored : 85.20 % 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: 1.62 (0.19), residues: 1920 helix: 1.68 (0.14), residues: 1280 sheet: 0.26 (0.54), residues: 88 loop : -0.11 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 281 HIS 0.006 0.002 HIS C 392 PHE 0.021 0.003 PHE D 186 TYR 0.030 0.004 TYR C 411 ARG 0.005 0.001 ARG B 297 *********************** 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 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 1.693 Fit side-chains REVERT: A 187 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7382 (tt) REVERT: A 257 VAL cc_start: 0.7484 (t) cc_final: 0.7048 (p) REVERT: A 283 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6755 (tp30) REVERT: A 287 MET cc_start: 0.4765 (ttp) cc_final: 0.3903 (tpt) REVERT: A 343 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7907 (tptm) REVERT: A 408 GLN cc_start: 0.8298 (mm110) cc_final: 0.8078 (mm-40) REVERT: A 433 ASP cc_start: 0.8397 (t70) cc_final: 0.8173 (t0) REVERT: A 473 MET cc_start: 0.5727 (tmm) cc_final: 0.5121 (tmm) REVERT: A 483 PHE cc_start: 0.6916 (t80) cc_final: 0.6668 (t80) REVERT: B 187 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7383 (tt) REVERT: B 257 VAL cc_start: 0.7484 (t) cc_final: 0.7047 (p) REVERT: B 283 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6743 (tp30) REVERT: B 287 MET cc_start: 0.4808 (ttp) cc_final: 0.3911 (tpt) REVERT: B 343 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7902 (tptm) REVERT: B 433 ASP cc_start: 0.8401 (t70) cc_final: 0.8175 (t0) REVERT: B 473 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5366 (tmm) REVERT: B 483 PHE cc_start: 0.6914 (t80) cc_final: 0.6671 (t80) REVERT: C 257 VAL cc_start: 0.7481 (t) cc_final: 0.7043 (p) REVERT: C 283 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6766 (tp30) REVERT: C 287 MET cc_start: 0.4790 (ttp) cc_final: 0.3912 (tpt) REVERT: C 343 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7899 (tptm) REVERT: C 408 GLN cc_start: 0.8283 (mm110) cc_final: 0.8063 (mm-40) REVERT: C 433 ASP cc_start: 0.8413 (t70) cc_final: 0.7960 (m-30) REVERT: C 483 PHE cc_start: 0.6909 (t80) cc_final: 0.6672 (t80) REVERT: D 187 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7378 (tt) REVERT: D 257 VAL cc_start: 0.7489 (t) cc_final: 0.7054 (p) REVERT: D 283 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6758 (tp30) REVERT: D 287 MET cc_start: 0.4810 (ttp) cc_final: 0.3904 (tpt) REVERT: D 433 ASP cc_start: 0.8415 (t70) cc_final: 0.7959 (m-30) REVERT: D 483 PHE cc_start: 0.6909 (t80) cc_final: 0.6664 (t80) outliers start: 31 outliers final: 18 residues processed: 267 average time/residue: 1.3633 time to fit residues: 399.0217 Evaluate side-chains 266 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE 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 485 THR Chi-restraints excluded: chain B residue 176 ILE 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 B residue 485 THR Chi-restraints excluded: chain C residue 176 ILE 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 176 ILE 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 494 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.169173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121578 restraints weight = 14962.777| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.62 r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15328 Z= 0.192 Angle : 0.522 7.834 20788 Z= 0.277 Chirality : 0.042 0.194 2348 Planarity : 0.003 0.023 2596 Dihedral : 7.185 58.908 2212 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 13.97 % Favored : 84.64 % 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: 2.01 (0.19), residues: 1920 helix: 1.98 (0.14), residues: 1284 sheet: 0.23 (0.54), residues: 88 loop : 0.06 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 281 HIS 0.004 0.001 HIS A 437 PHE 0.012 0.002 PHE B 389 TYR 0.021 0.002 TYR D 347 ARG 0.002 0.000 ARG C 504 *********************** 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 268 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.732 Fit side-chains REVERT: A 257 VAL cc_start: 0.7350 (t) cc_final: 0.6891 (p) REVERT: A 283 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6656 (tp30) REVERT: A 287 MET cc_start: 0.4428 (ttp) cc_final: 0.3436 (tpt) REVERT: A 343 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7889 (tptm) REVERT: A 408 GLN cc_start: 0.8274 (mm110) cc_final: 0.8058 (mm-40) REVERT: A 433 ASP cc_start: 0.8252 (t70) cc_final: 0.7988 (m-30) REVERT: A 459 GLU cc_start: 0.8242 (pt0) cc_final: 0.7917 (mt-10) REVERT: A 473 MET cc_start: 0.5687 (tmm) cc_final: 0.5191 (tmm) REVERT: A 483 PHE cc_start: 0.6967 (t80) cc_final: 0.6703 (t80) REVERT: B 257 VAL cc_start: 0.7355 (t) cc_final: 0.6892 (p) REVERT: B 283 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6650 (tp30) REVERT: B 287 MET cc_start: 0.4441 (ttp) cc_final: 0.3420 (tpt) REVERT: B 343 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7881 (tptm) REVERT: B 433 ASP cc_start: 0.8259 (t70) cc_final: 0.8019 (m-30) REVERT: B 459 GLU cc_start: 0.8249 (pt0) cc_final: 0.7919 (mt-10) REVERT: B 473 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5254 (tmm) REVERT: B 483 PHE cc_start: 0.6958 (t80) cc_final: 0.6717 (t80) REVERT: C 257 VAL cc_start: 0.7356 (t) cc_final: 0.6895 (p) REVERT: C 283 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6677 (tp30) REVERT: C 287 MET cc_start: 0.4438 (ttp) cc_final: 0.3437 (tpt) REVERT: C 343 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7884 (tptm) REVERT: C 408 GLN cc_start: 0.8275 (mm110) cc_final: 0.8052 (mm-40) REVERT: C 433 ASP cc_start: 0.8256 (t70) cc_final: 0.8009 (m-30) REVERT: C 459 GLU cc_start: 0.8234 (pt0) cc_final: 0.7929 (mt-10) REVERT: C 483 PHE cc_start: 0.6947 (t80) cc_final: 0.6699 (t80) REVERT: D 257 VAL cc_start: 0.7357 (t) cc_final: 0.6899 (p) REVERT: D 283 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6667 (tp30) REVERT: D 287 MET cc_start: 0.4445 (ttp) cc_final: 0.3431 (tpt) REVERT: D 433 ASP cc_start: 0.8260 (t70) cc_final: 0.8009 (m-30) REVERT: D 459 GLU cc_start: 0.8235 (pt0) cc_final: 0.7922 (mt-10) REVERT: D 483 PHE cc_start: 0.6958 (t80) cc_final: 0.6716 (t80) outliers start: 20 outliers final: 9 residues processed: 265 average time/residue: 1.3074 time to fit residues: 380.5161 Evaluate side-chains 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE 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 Chi-restraints excluded: chain D residue 370 SER 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: 5.9990 chunk 160 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.168609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121204 restraints weight = 14924.234| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.61 r_work: 0.3168 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15328 Z= 0.207 Angle : 0.535 8.946 20788 Z= 0.284 Chirality : 0.042 0.196 2348 Planarity : 0.003 0.022 2596 Dihedral : 6.927 58.073 2212 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 14.18 % Favored : 84.36 % 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: 2.17 (0.19), residues: 1920 helix: 2.10 (0.14), residues: 1284 sheet: 0.20 (0.53), residues: 88 loop : 0.14 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 373 HIS 0.004 0.001 HIS D 421 PHE 0.012 0.002 PHE B 389 TYR 0.028 0.002 TYR C 411 ARG 0.002 0.000 ARG A 126 *********************** 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 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 1.642 Fit side-chains REVERT: A 257 VAL cc_start: 0.7341 (t) cc_final: 0.6880 (p) REVERT: A 283 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6669 (tp30) REVERT: A 287 MET cc_start: 0.4545 (ttp) cc_final: 0.3571 (tpt) REVERT: A 343 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7897 (tptm) REVERT: A 408 GLN cc_start: 0.8256 (mm110) cc_final: 0.8037 (mm-40) REVERT: A 433 ASP cc_start: 0.8247 (t70) cc_final: 0.7963 (m-30) REVERT: A 459 GLU cc_start: 0.8237 (pt0) cc_final: 0.7934 (mt-10) REVERT: A 473 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5129 (tmm) REVERT: B 257 VAL cc_start: 0.7348 (t) cc_final: 0.6892 (p) REVERT: B 283 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6657 (tp30) REVERT: B 287 MET cc_start: 0.4558 (ttp) cc_final: 0.3564 (tpt) REVERT: B 343 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7892 (tptm) REVERT: B 433 ASP cc_start: 0.8268 (t70) cc_final: 0.8006 (m-30) REVERT: B 459 GLU cc_start: 0.8244 (pt0) cc_final: 0.7943 (mt-10) REVERT: B 473 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5377 (tmm) REVERT: B 483 PHE cc_start: 0.6982 (t80) cc_final: 0.6751 (t80) REVERT: C 257 VAL cc_start: 0.7347 (t) cc_final: 0.6884 (p) REVERT: C 283 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6672 (tp30) REVERT: C 287 MET cc_start: 0.4550 (ttp) cc_final: 0.3572 (tpt) REVERT: C 343 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7894 (tptm) REVERT: C 408 GLN cc_start: 0.8272 (mm110) cc_final: 0.8040 (mm-40) REVERT: C 433 ASP cc_start: 0.8261 (t70) cc_final: 0.8002 (m-30) REVERT: C 459 GLU cc_start: 0.8240 (pt0) cc_final: 0.7944 (mt-10) REVERT: C 483 PHE cc_start: 0.6977 (t80) cc_final: 0.6747 (t80) REVERT: D 257 VAL cc_start: 0.7338 (t) cc_final: 0.6880 (p) REVERT: D 283 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6668 (tp30) REVERT: D 287 MET cc_start: 0.4562 (ttp) cc_final: 0.3558 (tpt) REVERT: D 433 ASP cc_start: 0.8258 (t70) cc_final: 0.8001 (m-30) REVERT: D 459 GLU cc_start: 0.8232 (pt0) cc_final: 0.7937 (mt-10) REVERT: D 483 PHE cc_start: 0.6976 (t80) cc_final: 0.6747 (t80) outliers start: 21 outliers final: 11 residues processed: 263 average time/residue: 1.2767 time to fit residues: 369.5168 Evaluate side-chains 257 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 36 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.169348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121821 restraints weight = 15075.134| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.62 r_work: 0.3137 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15328 Z= 0.185 Angle : 0.522 9.431 20788 Z= 0.274 Chirality : 0.042 0.200 2348 Planarity : 0.003 0.022 2596 Dihedral : 6.524 56.634 2212 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.91 % Allowed : 15.22 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.19), residues: 1920 helix: 2.20 (0.14), residues: 1284 sheet: 0.11 (0.53), residues: 88 loop : 0.18 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 373 HIS 0.004 0.001 HIS B 437 PHE 0.011 0.002 PHE B 389 TYR 0.026 0.002 TYR C 411 ARG 0.002 0.000 ARG A 126 ********************** 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 248 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 1.638 Fit side-chains REVERT: A 257 VAL cc_start: 0.7335 (t) cc_final: 0.6869 (p) REVERT: A 283 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6574 (tp30) REVERT: A 287 MET cc_start: 0.4423 (ttp) cc_final: 0.3405 (tpt) REVERT: A 343 LYS cc_start: 0.8380 (mtmm) cc_final: 0.7884 (tptm) REVERT: A 408 GLN cc_start: 0.8261 (mm110) cc_final: 0.8047 (mm-40) REVERT: A 433 ASP cc_start: 0.8227 (t70) cc_final: 0.8013 (m-30) REVERT: A 459 GLU cc_start: 0.8233 (pt0) cc_final: 0.7923 (mt-10) REVERT: A 473 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5083 (tmm) REVERT: B 257 VAL cc_start: 0.7326 (t) cc_final: 0.6856 (p) REVERT: B 283 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6553 (tp30) REVERT: B 287 MET cc_start: 0.4439 (ttp) cc_final: 0.3394 (tpt) REVERT: B 343 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7885 (tptm) REVERT: B 433 ASP cc_start: 0.8258 (t70) cc_final: 0.8011 (m-30) REVERT: B 459 GLU cc_start: 0.8241 (pt0) cc_final: 0.7930 (mt-10) REVERT: B 473 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5307 (tmm) REVERT: C 257 VAL cc_start: 0.7333 (t) cc_final: 0.6867 (p) REVERT: C 283 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6580 (tp30) REVERT: C 287 MET cc_start: 0.4430 (ttp) cc_final: 0.3409 (tpt) REVERT: C 343 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7883 (tptm) REVERT: C 408 GLN cc_start: 0.8278 (mm110) cc_final: 0.8072 (mm-40) REVERT: C 433 ASP cc_start: 0.8250 (t70) cc_final: 0.8008 (m-30) REVERT: C 459 GLU cc_start: 0.8238 (pt0) cc_final: 0.7924 (mt-10) REVERT: C 473 MET cc_start: 0.5617 (tmt) cc_final: 0.5167 (tmm) REVERT: D 257 VAL cc_start: 0.7330 (t) cc_final: 0.6858 (p) REVERT: D 283 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6581 (tp30) REVERT: D 287 MET cc_start: 0.4433 (ttp) cc_final: 0.3398 (tpt) REVERT: D 433 ASP cc_start: 0.8259 (t70) cc_final: 0.8007 (m-30) REVERT: D 459 GLU cc_start: 0.8231 (pt0) cc_final: 0.7927 (mt-10) REVERT: D 473 MET cc_start: 0.5615 (tmt) cc_final: 0.5168 (tmm) outliers start: 13 outliers final: 11 residues processed: 246 average time/residue: 1.3364 time to fit residues: 361.8524 Evaluate side-chains 242 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123376 restraints weight = 15073.809| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.62 r_work: 0.3159 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15328 Z= 0.150 Angle : 0.498 9.958 20788 Z= 0.260 Chirality : 0.041 0.194 2348 Planarity : 0.003 0.024 2596 Dihedral : 5.982 53.765 2212 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.54 % Allowed : 14.80 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.19), residues: 1920 helix: 2.31 (0.14), residues: 1288 sheet: 0.11 (0.52), residues: 88 loop : 0.35 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 373 HIS 0.004 0.001 HIS A 437 PHE 0.009 0.001 PHE B 389 TYR 0.022 0.002 TYR C 411 ARG 0.002 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13426.43 seconds wall clock time: 238 minutes 14.83 seconds (14294.83 seconds total)