Starting phenix.real_space_refine on Sat Aug 23 21:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc6_44425/08_2025/9bc6_44425.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc6_44425/08_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_44425/08_2025/9bc6_44425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc6_44425/08_2025/9bc6_44425.map" model { file = "/net/cci-nas-00/data/ceres_data/9bc6_44425/08_2025/9bc6_44425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc6_44425/08_2025/9bc6_44425.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 9, 'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 13, 'GLN:plan1': 1, 'ASP:plan': 10, 'ASN:plan1': 3} 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: 2.90, per 1000 atoms: 0.19 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: 1.18 Conformation dependent library (CDL) restraints added in 571.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 1.85 Time building geometry restraints manager: 1.48 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: 0.01 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.092 15328 Z= 0.712 Angle : 1.767 12.741 20788 Z= 1.208 Chirality : 0.093 0.373 2348 Planarity : 0.014 0.092 2596 Dihedral : 12.254 85.343 5320 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.56 % Allowed : 2.51 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG D 142 TYR 0.119 0.022 TYR D 407 PHE 0.066 0.013 PHE A 186 TRP 0.158 0.027 TRP B 281 HIS 0.019 0.005 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.01157 (15328) covalent geometry : angle 1.76655 (20788) hydrogen bonds : bond 0.19323 ( 989) hydrogen bonds : angle 6.89939 ( 2871) *********************** 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 : 0.490 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: 0.5495 time to fit residues: 196.5643 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 : 0.410 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.170973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122857 restraints weight = 14857.996| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.63 r_work: 0.3165 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15328 Z= 0.140 Angle : 0.556 6.482 20788 Z= 0.303 Chirality : 0.043 0.155 2348 Planarity : 0.004 0.027 2596 Dihedral : 8.154 53.672 2236 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 7.96 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.19), residues: 1920 helix: 1.33 (0.14), residues: 1300 sheet: 0.44 (0.55), residues: 88 loop : 0.41 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 504 TYR 0.015 0.002 TYR B 407 PHE 0.017 0.002 PHE A 569 TRP 0.028 0.002 TRP B 281 HIS 0.005 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00292 (15328) covalent geometry : angle 0.55581 (20788) hydrogen bonds : bond 0.05022 ( 989) hydrogen bonds : angle 4.32065 ( 2871) *********************** 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 319 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 0.388 Fit side-chains REVERT: A 195 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6730 (mmp-170) REVERT: A 257 VAL cc_start: 0.7575 (t) cc_final: 0.7191 (p) REVERT: A 283 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6705 (tp30) REVERT: A 287 MET cc_start: 0.4351 (ttp) cc_final: 0.3370 (tpt) REVERT: A 304 MET cc_start: 0.8663 (tpp) cc_final: 0.8397 (tpp) REVERT: A 343 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7933 (tptm) REVERT: A 408 GLN cc_start: 0.8250 (mm110) cc_final: 0.8042 (mm-40) REVERT: A 422 LYS cc_start: 0.8709 (mttp) cc_final: 0.8494 (mttt) REVERT: A 433 ASP cc_start: 0.8252 (t70) cc_final: 0.7996 (m-30) REVERT: A 459 GLU cc_start: 0.8415 (pt0) cc_final: 0.7995 (pp20) REVERT: A 483 PHE cc_start: 0.7122 (t80) cc_final: 0.6851 (t80) REVERT: B 195 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6699 (mmp-170) REVERT: B 257 VAL cc_start: 0.7565 (t) cc_final: 0.7179 (p) REVERT: B 283 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6727 (tp30) REVERT: B 287 MET cc_start: 0.4354 (ttp) cc_final: 0.3367 (tpt) REVERT: B 304 MET cc_start: 0.8668 (tpp) cc_final: 0.8402 (tpp) REVERT: B 343 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7921 (tptm) REVERT: B 408 GLN cc_start: 0.8246 (mm110) cc_final: 0.8043 (mm-40) REVERT: B 422 LYS cc_start: 0.8704 (mttp) cc_final: 0.8486 (mttt) REVERT: B 433 ASP cc_start: 0.8248 (t70) cc_final: 0.7994 (m-30) REVERT: B 459 GLU cc_start: 0.8405 (pt0) cc_final: 0.7938 (mt-10) REVERT: B 483 PHE cc_start: 0.7125 (t80) cc_final: 0.6852 (t80) REVERT: C 195 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6597 (mmp-170) REVERT: C 257 VAL cc_start: 0.7563 (t) cc_final: 0.7182 (p) REVERT: C 283 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6710 (tp30) REVERT: C 287 MET cc_start: 0.4358 (ttp) cc_final: 0.3368 (tpt) REVERT: C 304 MET cc_start: 0.8677 (tpp) cc_final: 0.8415 (tpp) REVERT: C 343 LYS cc_start: 0.8423 (mtmm) cc_final: 0.7926 (tptm) REVERT: C 408 GLN cc_start: 0.8234 (mm110) cc_final: 0.8033 (mm-40) REVERT: C 422 LYS cc_start: 0.8685 (mttp) cc_final: 0.8463 (mttt) REVERT: C 433 ASP cc_start: 0.8255 (t70) cc_final: 0.8005 (m-30) REVERT: C 459 GLU cc_start: 0.8394 (pt0) cc_final: 0.7939 (mt-10) REVERT: C 483 PHE cc_start: 0.7121 (t80) cc_final: 0.6828 (t80) REVERT: D 195 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6726 (mmp-170) REVERT: D 257 VAL cc_start: 0.7558 (t) cc_final: 0.7170 (p) REVERT: D 283 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6705 (tp30) REVERT: D 287 MET cc_start: 0.4360 (ttp) cc_final: 0.3373 (tpt) REVERT: D 304 MET cc_start: 0.8670 (tpp) cc_final: 0.8406 (tpp) REVERT: D 343 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7880 (tptt) REVERT: D 408 GLN cc_start: 0.8237 (mm110) cc_final: 0.8036 (mm-40) REVERT: D 422 LYS cc_start: 0.8684 (mttp) cc_final: 0.8463 (mttt) REVERT: D 433 ASP cc_start: 0.8251 (t70) cc_final: 0.8005 (m-30) REVERT: D 459 GLU cc_start: 0.8395 (pt0) cc_final: 0.7938 (mt-10) REVERT: D 483 PHE cc_start: 0.7119 (t80) cc_final: 0.6832 (t80) outliers start: 28 outliers final: 4 residues processed: 303 average time/residue: 0.5459 time to fit residues: 181.7135 Evaluate side-chains 266 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 258 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 48 optimal weight: 20.0000 chunk 58 optimal weight: 0.0370 chunk 151 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 568 ASN B 398 GLN B 568 ASN C 398 GLN C 568 ASN D 398 GLN D 568 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119488 restraints weight = 14997.246| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.62 r_work: 0.3119 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15328 Z= 0.218 Angle : 0.612 6.925 20788 Z= 0.330 Chirality : 0.046 0.170 2348 Planarity : 0.004 0.032 2596 Dihedral : 8.502 56.438 2228 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.21 % Allowed : 9.78 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 1920 helix: 1.57 (0.14), residues: 1272 sheet: 0.52 (0.54), residues: 88 loop : 0.25 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 504 TYR 0.026 0.003 TYR D 347 PHE 0.019 0.003 PHE A 186 TRP 0.031 0.003 TRP B 281 HIS 0.004 0.002 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00516 (15328) covalent geometry : angle 0.61161 (20788) hydrogen bonds : bond 0.05862 ( 989) hydrogen bonds : angle 4.36211 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.599 Fit side-chains REVERT: A 257 VAL cc_start: 0.7574 (t) cc_final: 0.7194 (p) REVERT: A 283 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6755 (tp30) REVERT: A 287 MET cc_start: 0.4776 (ttp) cc_final: 0.3801 (tpt) REVERT: A 343 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7926 (tptm) REVERT: A 408 GLN cc_start: 0.8267 (mm110) cc_final: 0.8066 (mm-40) REVERT: A 433 ASP cc_start: 0.8353 (t70) cc_final: 0.7970 (m-30) REVERT: A 459 GLU cc_start: 0.8472 (pt0) cc_final: 0.8005 (mt-10) REVERT: A 483 PHE cc_start: 0.7077 (t80) cc_final: 0.6804 (t80) REVERT: B 257 VAL cc_start: 0.7574 (t) cc_final: 0.7201 (p) REVERT: B 283 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6745 (tp30) REVERT: B 287 MET cc_start: 0.4757 (ttp) cc_final: 0.3769 (tpt) REVERT: B 343 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7923 (tptm) REVERT: B 408 GLN cc_start: 0.8264 (mm110) cc_final: 0.8064 (mm-40) REVERT: B 433 ASP cc_start: 0.8357 (t70) cc_final: 0.7972 (m-30) REVERT: B 459 GLU cc_start: 0.8478 (pt0) cc_final: 0.8012 (mt-10) REVERT: B 483 PHE cc_start: 0.7071 (t80) cc_final: 0.6799 (t80) REVERT: C 257 VAL cc_start: 0.7572 (t) cc_final: 0.7195 (p) REVERT: C 283 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6750 (tp30) REVERT: C 287 MET cc_start: 0.4767 (ttp) cc_final: 0.3789 (tpt) REVERT: C 343 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7895 (tptm) REVERT: C 408 GLN cc_start: 0.8270 (mm110) cc_final: 0.8040 (mm-40) REVERT: C 433 ASP cc_start: 0.8364 (t70) cc_final: 0.7961 (m-30) REVERT: C 459 GLU cc_start: 0.8470 (pt0) cc_final: 0.8007 (mt-10) REVERT: C 483 PHE cc_start: 0.7068 (t80) cc_final: 0.6804 (t80) REVERT: D 257 VAL cc_start: 0.7573 (t) cc_final: 0.7187 (p) REVERT: D 283 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6754 (tp30) REVERT: D 287 MET cc_start: 0.4758 (ttp) cc_final: 0.3772 (tpt) REVERT: D 408 GLN cc_start: 0.8261 (mm110) cc_final: 0.8034 (mm-40) REVERT: D 433 ASP cc_start: 0.8366 (t70) cc_final: 0.7961 (m-30) REVERT: D 459 GLU cc_start: 0.8475 (pt0) cc_final: 0.8007 (mt-10) REVERT: D 483 PHE cc_start: 0.7061 (t80) cc_final: 0.6803 (t80) outliers start: 46 outliers final: 20 residues processed: 302 average time/residue: 0.5551 time to fit residues: 183.1926 Evaluate side-chains 260 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 523 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.168407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120414 restraints weight = 14926.141| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.62 r_work: 0.3122 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15328 Z= 0.170 Angle : 0.550 6.467 20788 Z= 0.298 Chirality : 0.043 0.166 2348 Planarity : 0.004 0.036 2596 Dihedral : 7.591 56.249 2212 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.86 % Allowed : 10.41 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 1920 helix: 1.76 (0.14), residues: 1272 sheet: 0.46 (0.54), residues: 88 loop : 0.14 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 126 TYR 0.021 0.002 TYR D 347 PHE 0.014 0.002 PHE C 389 TRP 0.029 0.002 TRP C 281 HIS 0.004 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00394 (15328) covalent geometry : angle 0.55021 (20788) hydrogen bonds : bond 0.05284 ( 989) hydrogen bonds : angle 4.22304 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.436 Fit side-chains REVERT: A 257 VAL cc_start: 0.7550 (t) cc_final: 0.7141 (p) REVERT: A 283 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6710 (tp30) REVERT: A 287 MET cc_start: 0.4590 (ttp) cc_final: 0.3663 (tpt) REVERT: A 343 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7892 (tptm) REVERT: A 408 GLN cc_start: 0.8269 (mm110) cc_final: 0.8062 (mm-40) REVERT: A 433 ASP cc_start: 0.8304 (t70) cc_final: 0.7972 (m-30) REVERT: A 459 GLU cc_start: 0.8413 (pt0) cc_final: 0.7983 (mt-10) REVERT: A 483 PHE cc_start: 0.6982 (t80) cc_final: 0.6687 (t80) REVERT: B 257 VAL cc_start: 0.7557 (t) cc_final: 0.7151 (p) REVERT: B 283 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6725 (tp30) REVERT: B 287 MET cc_start: 0.4602 (ttp) cc_final: 0.3657 (tpt) REVERT: B 343 LYS cc_start: 0.8391 (mtmm) cc_final: 0.7896 (tptm) REVERT: B 408 GLN cc_start: 0.8263 (mm110) cc_final: 0.8056 (mm-40) REVERT: B 433 ASP cc_start: 0.8307 (t70) cc_final: 0.7971 (m-30) REVERT: B 459 GLU cc_start: 0.8417 (pt0) cc_final: 0.7989 (mt-10) REVERT: B 483 PHE cc_start: 0.6984 (t80) cc_final: 0.6691 (t80) REVERT: C 257 VAL cc_start: 0.7548 (t) cc_final: 0.7138 (p) REVERT: C 283 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6728 (tp30) REVERT: C 287 MET cc_start: 0.4600 (ttp) cc_final: 0.3655 (tpt) REVERT: C 343 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7875 (tptm) REVERT: C 408 GLN cc_start: 0.8260 (mm110) cc_final: 0.8054 (mm-40) REVERT: C 433 ASP cc_start: 0.8322 (t70) cc_final: 0.7972 (m-30) REVERT: C 459 GLU cc_start: 0.8406 (pt0) cc_final: 0.7988 (mt-10) REVERT: C 483 PHE cc_start: 0.6970 (t80) cc_final: 0.6670 (t80) REVERT: D 257 VAL cc_start: 0.7557 (t) cc_final: 0.7150 (p) REVERT: D 283 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6724 (tp30) REVERT: D 287 MET cc_start: 0.4606 (ttp) cc_final: 0.3653 (tpt) REVERT: D 408 GLN cc_start: 0.8251 (mm110) cc_final: 0.8047 (mm-40) REVERT: D 433 ASP cc_start: 0.8320 (t70) cc_final: 0.7972 (m-30) REVERT: D 459 GLU cc_start: 0.8414 (pt0) cc_final: 0.7988 (mt-10) REVERT: D 483 PHE cc_start: 0.6972 (t80) cc_final: 0.6673 (t80) outliers start: 41 outliers final: 16 residues processed: 283 average time/residue: 0.5258 time to fit residues: 163.9435 Evaluate side-chains 256 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 485 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 133 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.169174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121245 restraints weight = 15063.616| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.63 r_work: 0.3127 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2518 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= 0.140 Angle : 0.516 6.040 20788 Z= 0.276 Chirality : 0.042 0.171 2348 Planarity : 0.003 0.023 2596 Dihedral : 7.084 55.321 2212 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.75 % Allowed : 13.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.19), residues: 1920 helix: 1.97 (0.14), residues: 1280 sheet: 0.50 (0.54), residues: 88 loop : 0.15 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.021 0.002 TYR D 347 PHE 0.012 0.002 PHE C 389 TRP 0.027 0.002 TRP C 281 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00311 (15328) covalent geometry : angle 0.51574 (20788) hydrogen bonds : bond 0.04841 ( 989) hydrogen bonds : angle 4.09281 ( 2871) *********************** 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 281 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.442 Fit side-chains REVERT: A 257 VAL cc_start: 0.7456 (t) cc_final: 0.7030 (p) REVERT: A 283 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6706 (tp30) REVERT: A 287 MET cc_start: 0.4515 (ttp) cc_final: 0.3536 (tpt) REVERT: A 343 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7885 (tptm) REVERT: A 408 GLN cc_start: 0.8266 (mm110) cc_final: 0.8053 (mm-40) REVERT: A 433 ASP cc_start: 0.8279 (t70) cc_final: 0.7985 (m-30) REVERT: A 459 GLU cc_start: 0.8367 (pt0) cc_final: 0.7959 (mt-10) REVERT: A 483 PHE cc_start: 0.6963 (t80) cc_final: 0.6679 (t80) REVERT: B 257 VAL cc_start: 0.7440 (t) cc_final: 0.7012 (p) REVERT: B 283 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6698 (tp30) REVERT: B 287 MET cc_start: 0.4526 (ttp) cc_final: 0.3541 (tpt) REVERT: B 343 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7888 (tptm) REVERT: B 408 GLN cc_start: 0.8273 (mm110) cc_final: 0.8061 (mm-40) REVERT: B 433 ASP cc_start: 0.8269 (t70) cc_final: 0.7982 (m-30) REVERT: B 459 GLU cc_start: 0.8354 (pt0) cc_final: 0.7952 (mt-10) REVERT: B 473 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6075 (tmm) REVERT: B 483 PHE cc_start: 0.6956 (t80) cc_final: 0.6676 (t80) REVERT: C 257 VAL cc_start: 0.7431 (t) cc_final: 0.7003 (p) REVERT: C 283 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6702 (tp30) REVERT: C 287 MET cc_start: 0.4517 (ttp) cc_final: 0.3537 (tpt) REVERT: C 343 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7882 (tptm) REVERT: C 408 GLN cc_start: 0.8267 (mm110) cc_final: 0.8054 (mm-40) REVERT: C 433 ASP cc_start: 0.8270 (t70) cc_final: 0.7967 (m-30) REVERT: C 459 GLU cc_start: 0.8355 (pt0) cc_final: 0.7955 (mt-10) REVERT: C 483 PHE cc_start: 0.6925 (t80) cc_final: 0.6641 (t80) REVERT: D 257 VAL cc_start: 0.7445 (t) cc_final: 0.7017 (p) REVERT: D 283 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6705 (tp30) REVERT: D 287 MET cc_start: 0.4528 (ttp) cc_final: 0.3536 (tpt) REVERT: D 343 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8078 (mptt) REVERT: D 408 GLN cc_start: 0.8265 (mm110) cc_final: 0.8054 (mm-40) REVERT: D 433 ASP cc_start: 0.8269 (t70) cc_final: 0.7963 (m-30) REVERT: D 459 GLU cc_start: 0.8361 (pt0) cc_final: 0.7955 (mt-10) REVERT: D 483 PHE cc_start: 0.6942 (t80) cc_final: 0.6659 (t80) outliers start: 25 outliers final: 8 residues processed: 273 average time/residue: 0.5354 time to fit residues: 160.6066 Evaluate side-chains 235 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 178 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 398 GLN B 156 ASN B 398 GLN C 156 ASN C 398 GLN D 156 ASN D 398 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118985 restraints weight = 14905.569| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.62 r_work: 0.3099 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15328 Z= 0.223 Angle : 0.626 7.310 20788 Z= 0.334 Chirality : 0.046 0.182 2348 Planarity : 0.004 0.026 2596 Dihedral : 8.034 57.144 2212 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 12.71 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.19), residues: 1920 helix: 1.76 (0.14), residues: 1280 sheet: 0.34 (0.54), residues: 88 loop : -0.10 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 126 TYR 0.026 0.003 TYR C 347 PHE 0.017 0.003 PHE C 186 TRP 0.031 0.003 TRP C 281 HIS 0.005 0.002 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00531 (15328) covalent geometry : angle 0.62551 (20788) hydrogen bonds : bond 0.05893 ( 989) hydrogen bonds : angle 4.29828 ( 2871) *********************** 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: 31 poor density : 249 time to evaluate : 0.492 Fit side-chains REVERT: A 187 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7291 (tt) REVERT: A 257 VAL cc_start: 0.7521 (t) cc_final: 0.7081 (p) REVERT: A 283 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6741 (tp30) REVERT: A 287 MET cc_start: 0.4655 (ttp) cc_final: 0.3708 (tpt) REVERT: A 343 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7893 (tptm) REVERT: A 408 GLN cc_start: 0.8279 (mm110) cc_final: 0.8061 (mm-40) REVERT: A 433 ASP cc_start: 0.8358 (t70) cc_final: 0.7967 (m-30) REVERT: A 459 GLU cc_start: 0.8353 (pt0) cc_final: 0.8004 (mt-10) REVERT: A 483 PHE cc_start: 0.6907 (t80) cc_final: 0.6699 (t80) REVERT: B 187 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7283 (tt) REVERT: B 257 VAL cc_start: 0.7487 (t) cc_final: 0.7052 (p) REVERT: B 283 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6739 (tp30) REVERT: B 287 MET cc_start: 0.4674 (ttp) cc_final: 0.3716 (tpt) REVERT: B 343 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7892 (tptm) REVERT: B 408 GLN cc_start: 0.8279 (mm110) cc_final: 0.8072 (mm-40) REVERT: B 433 ASP cc_start: 0.8356 (t70) cc_final: 0.7966 (m-30) REVERT: B 459 GLU cc_start: 0.8355 (pt0) cc_final: 0.8005 (mt-10) REVERT: B 483 PHE cc_start: 0.6901 (t80) cc_final: 0.6697 (t80) REVERT: C 187 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7292 (tt) REVERT: C 257 VAL cc_start: 0.7482 (t) cc_final: 0.7049 (p) REVERT: C 283 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6761 (tp30) REVERT: C 287 MET cc_start: 0.4666 (ttp) cc_final: 0.3763 (tpt) REVERT: C 343 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7877 (tptm) REVERT: C 408 GLN cc_start: 0.8270 (mm110) cc_final: 0.8051 (mm-40) REVERT: C 433 ASP cc_start: 0.8361 (t70) cc_final: 0.7953 (m-30) REVERT: C 459 GLU cc_start: 0.8354 (pt0) cc_final: 0.8002 (mt-10) REVERT: C 483 PHE cc_start: 0.6896 (t80) cc_final: 0.6692 (t80) REVERT: D 187 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7292 (tt) REVERT: D 257 VAL cc_start: 0.7489 (t) cc_final: 0.7057 (p) REVERT: D 283 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6749 (tp30) REVERT: D 287 MET cc_start: 0.4664 (ttp) cc_final: 0.3710 (tpt) REVERT: D 408 GLN cc_start: 0.8270 (mm110) cc_final: 0.8053 (mm-40) REVERT: D 433 ASP cc_start: 0.8357 (t70) cc_final: 0.7952 (m-30) REVERT: D 459 GLU cc_start: 0.8341 (pt0) cc_final: 0.7995 (mt-10) REVERT: D 483 PHE cc_start: 0.6907 (t80) cc_final: 0.6701 (t80) outliers start: 31 outliers final: 15 residues processed: 272 average time/residue: 0.5331 time to fit residues: 158.9421 Evaluate side-chains 262 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123631 restraints weight = 14912.142| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.61 r_work: 0.3164 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15328 Z= 0.109 Angle : 0.485 7.255 20788 Z= 0.255 Chirality : 0.041 0.190 2348 Planarity : 0.003 0.026 2596 Dihedral : 6.403 55.040 2212 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.91 % Allowed : 14.53 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.19), residues: 1920 helix: 2.14 (0.14), residues: 1284 sheet: 0.30 (0.53), residues: 88 loop : 0.20 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.026 0.001 TYR D 411 PHE 0.009 0.001 PHE C 389 TRP 0.026 0.002 TRP C 281 HIS 0.004 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00225 (15328) covalent geometry : angle 0.48507 (20788) hydrogen bonds : bond 0.04101 ( 989) hydrogen bonds : angle 3.93919 ( 2871) *********************** 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 260 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.480 Fit side-chains REVERT: A 208 LEU cc_start: 0.6573 (mt) cc_final: 0.6262 (mt) REVERT: A 257 VAL cc_start: 0.7331 (t) cc_final: 0.6872 (p) REVERT: A 283 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6656 (tp30) REVERT: A 287 MET cc_start: 0.4190 (ttp) cc_final: 0.3131 (tpt) REVERT: A 343 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7890 (tptm) REVERT: A 408 GLN cc_start: 0.8276 (mm110) cc_final: 0.8054 (mm-40) REVERT: A 459 GLU cc_start: 0.8336 (pt0) cc_final: 0.7968 (mt-10) REVERT: A 483 PHE cc_start: 0.6977 (t80) cc_final: 0.6745 (t80) REVERT: B 208 LEU cc_start: 0.6570 (mt) cc_final: 0.6258 (mt) REVERT: B 257 VAL cc_start: 0.7326 (t) cc_final: 0.6870 (p) REVERT: B 283 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6673 (tp30) REVERT: B 287 MET cc_start: 0.4208 (ttp) cc_final: 0.3131 (tpt) REVERT: B 343 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7898 (tptm) REVERT: B 408 GLN cc_start: 0.8278 (mm110) cc_final: 0.8075 (mm-40) REVERT: B 459 GLU cc_start: 0.8338 (pt0) cc_final: 0.7965 (mt-10) REVERT: B 483 PHE cc_start: 0.6970 (t80) cc_final: 0.6745 (t80) REVERT: C 208 LEU cc_start: 0.6590 (mt) cc_final: 0.6285 (mt) REVERT: C 257 VAL cc_start: 0.7328 (t) cc_final: 0.6871 (p) REVERT: C 283 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6630 (tp30) REVERT: C 287 MET cc_start: 0.4213 (ttp) cc_final: 0.3151 (tpt) REVERT: C 343 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7874 (tptm) REVERT: C 408 GLN cc_start: 0.8288 (mm110) cc_final: 0.8068 (mm-40) REVERT: C 459 GLU cc_start: 0.8330 (pt0) cc_final: 0.7960 (mt-10) REVERT: C 483 PHE cc_start: 0.6973 (t80) cc_final: 0.6743 (t80) REVERT: D 208 LEU cc_start: 0.6592 (mt) cc_final: 0.6282 (mt) REVERT: D 257 VAL cc_start: 0.7333 (t) cc_final: 0.6874 (p) REVERT: D 283 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6657 (tp30) REVERT: D 287 MET cc_start: 0.4205 (ttp) cc_final: 0.3139 (tpt) REVERT: D 343 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8079 (mptt) REVERT: D 408 GLN cc_start: 0.8280 (mm110) cc_final: 0.8061 (mm-40) REVERT: D 459 GLU cc_start: 0.8331 (pt0) cc_final: 0.7963 (mt-10) REVERT: D 483 PHE cc_start: 0.6981 (t80) cc_final: 0.6750 (t80) outliers start: 13 outliers final: 6 residues processed: 255 average time/residue: 0.5106 time to fit residues: 144.0339 Evaluate side-chains 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 111 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.171142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123876 restraints weight = 15095.149| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.61 r_work: 0.3167 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15328 Z= 0.106 Angle : 0.481 7.986 20788 Z= 0.252 Chirality : 0.040 0.186 2348 Planarity : 0.003 0.024 2596 Dihedral : 5.987 52.333 2212 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.40 % Allowed : 14.80 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.19), residues: 1920 helix: 2.29 (0.14), residues: 1288 sheet: 0.33 (0.53), residues: 88 loop : 0.36 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 504 TYR 0.027 0.001 TYR A 411 PHE 0.009 0.001 PHE C 389 TRP 0.024 0.001 TRP C 281 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00218 (15328) covalent geometry : angle 0.48096 (20788) hydrogen bonds : bond 0.04049 ( 989) hydrogen bonds : angle 3.84997 ( 2871) *********************** 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 262 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.592 Fit side-chains REVERT: A 257 VAL cc_start: 0.7325 (t) cc_final: 0.6866 (p) REVERT: A 283 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6544 (tp30) REVERT: A 287 MET cc_start: 0.4240 (ttp) cc_final: 0.3162 (tpt) REVERT: A 343 LYS cc_start: 0.8355 (mtmm) cc_final: 0.7877 (tptm) REVERT: A 459 GLU cc_start: 0.8351 (pt0) cc_final: 0.7978 (mt-10) REVERT: B 257 VAL cc_start: 0.7320 (t) cc_final: 0.6858 (p) REVERT: B 283 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6545 (tp30) REVERT: B 287 MET cc_start: 0.4256 (ttp) cc_final: 0.3165 (tpt) REVERT: B 343 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7891 (tptm) REVERT: B 429 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7872 (tp40) REVERT: B 459 GLU cc_start: 0.8366 (pt0) cc_final: 0.7982 (mt-10) REVERT: C 257 VAL cc_start: 0.7317 (t) cc_final: 0.6858 (p) REVERT: C 283 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6617 (tp30) REVERT: C 287 MET cc_start: 0.4252 (ttp) cc_final: 0.3169 (tpt) REVERT: C 343 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7873 (tptm) REVERT: C 459 GLU cc_start: 0.8349 (pt0) cc_final: 0.7978 (mt-10) REVERT: D 257 VAL cc_start: 0.7322 (t) cc_final: 0.6863 (p) REVERT: D 283 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6543 (tp30) REVERT: D 287 MET cc_start: 0.4243 (ttp) cc_final: 0.3106 (tpt) REVERT: D 343 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8082 (mptt) REVERT: D 459 GLU cc_start: 0.8357 (pt0) cc_final: 0.7981 (mt-10) outliers start: 20 outliers final: 9 residues processed: 254 average time/residue: 0.4842 time to fit residues: 135.7841 Evaluate side-chains 245 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS D 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119639 restraints weight = 14994.468| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.61 r_work: 0.3109 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15328 Z= 0.214 Angle : 0.623 9.280 20788 Z= 0.329 Chirality : 0.046 0.200 2348 Planarity : 0.004 0.024 2596 Dihedral : 7.569 57.366 2212 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.40 % Allowed : 14.80 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.19), residues: 1920 helix: 2.00 (0.14), residues: 1284 sheet: 0.34 (0.55), residues: 88 loop : -0.05 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 554 TYR 0.036 0.003 TYR A 411 PHE 0.016 0.002 PHE C 186 TRP 0.031 0.003 TRP C 281 HIS 0.005 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00509 (15328) covalent geometry : angle 0.62294 (20788) hydrogen bonds : bond 0.05662 ( 989) hydrogen bonds : angle 4.18356 ( 2871) *********************** 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 259 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.588 Fit side-chains REVERT: A 257 VAL cc_start: 0.7389 (t) cc_final: 0.6950 (p) REVERT: A 283 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6665 (tp30) REVERT: A 287 MET cc_start: 0.4721 (ttp) cc_final: 0.3736 (tpt) REVERT: A 343 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7890 (tptm) REVERT: A 459 GLU cc_start: 0.8359 (pt0) cc_final: 0.8029 (mt-10) REVERT: B 257 VAL cc_start: 0.7385 (t) cc_final: 0.6943 (p) REVERT: B 283 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6663 (tp30) REVERT: B 287 MET cc_start: 0.4744 (ttp) cc_final: 0.3747 (tpt) REVERT: B 343 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7899 (tptm) REVERT: B 459 GLU cc_start: 0.8367 (pt0) cc_final: 0.8029 (mt-10) REVERT: B 473 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5476 (tmt) REVERT: C 257 VAL cc_start: 0.7378 (t) cc_final: 0.6930 (p) REVERT: C 283 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6752 (tp30) REVERT: C 287 MET cc_start: 0.4731 (ttp) cc_final: 0.3743 (tpt) REVERT: C 343 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7898 (tptm) REVERT: C 459 GLU cc_start: 0.8359 (pt0) cc_final: 0.8030 (mt-10) REVERT: D 257 VAL cc_start: 0.7377 (t) cc_final: 0.6930 (p) REVERT: D 283 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6670 (tp30) REVERT: D 287 MET cc_start: 0.4728 (ttp) cc_final: 0.3739 (tpt) REVERT: D 343 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8110 (mptt) REVERT: D 459 GLU cc_start: 0.8366 (pt0) cc_final: 0.8035 (mt-10) outliers start: 20 outliers final: 9 residues processed: 255 average time/residue: 0.5098 time to fit residues: 143.4529 Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain 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 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 16 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.169503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122073 restraints weight = 15055.344| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.61 r_work: 0.3141 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2894 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= 0.126 Angle : 0.526 10.225 20788 Z= 0.275 Chirality : 0.042 0.195 2348 Planarity : 0.003 0.023 2596 Dihedral : 6.664 58.366 2212 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.70 % Allowed : 15.78 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.19), residues: 1920 helix: 2.20 (0.14), residues: 1284 sheet: 0.19 (0.53), residues: 88 loop : 0.04 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.031 0.002 TYR A 411 PHE 0.011 0.001 PHE C 389 TRP 0.031 0.002 TRP C 281 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00271 (15328) covalent geometry : angle 0.52563 (20788) hydrogen bonds : bond 0.04533 ( 989) hydrogen bonds : angle 3.99016 ( 2871) ********************** 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: 10 poor density : 238 time to evaluate : 0.500 Fit side-chains REVERT: A 208 LEU cc_start: 0.6625 (mt) cc_final: 0.6262 (mt) REVERT: A 257 VAL cc_start: 0.7332 (t) cc_final: 0.6873 (p) REVERT: A 283 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6599 (tp30) REVERT: A 287 MET cc_start: 0.4405 (ttp) cc_final: 0.3370 (tpt) REVERT: A 343 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7889 (tptm) REVERT: A 459 GLU cc_start: 0.8359 (pt0) cc_final: 0.8011 (mt-10) REVERT: B 208 LEU cc_start: 0.6613 (mt) cc_final: 0.6254 (mt) REVERT: B 257 VAL cc_start: 0.7339 (t) cc_final: 0.6880 (p) REVERT: B 283 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6593 (tp30) REVERT: B 287 MET cc_start: 0.4433 (ttp) cc_final: 0.3375 (tpt) REVERT: B 343 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7895 (tptm) REVERT: B 459 GLU cc_start: 0.8353 (pt0) cc_final: 0.8009 (mt-10) REVERT: B 473 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5139 (tmm) REVERT: C 208 LEU cc_start: 0.6607 (mt) cc_final: 0.6253 (mt) REVERT: C 257 VAL cc_start: 0.7336 (t) cc_final: 0.6876 (p) REVERT: C 283 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6684 (tp30) REVERT: C 287 MET cc_start: 0.4398 (ttp) cc_final: 0.3382 (tpt) REVERT: C 343 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7886 (tptm) REVERT: C 459 GLU cc_start: 0.8346 (pt0) cc_final: 0.8007 (mt-10) REVERT: D 208 LEU cc_start: 0.6599 (mt) cc_final: 0.6239 (mt) REVERT: D 257 VAL cc_start: 0.7343 (t) cc_final: 0.6886 (p) REVERT: D 283 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6599 (tp30) REVERT: D 287 MET cc_start: 0.4408 (ttp) cc_final: 0.3382 (tpt) REVERT: D 343 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8082 (mptt) REVERT: D 459 GLU cc_start: 0.8353 (pt0) cc_final: 0.8010 (mt-10) REVERT: D 473 MET cc_start: 0.5682 (tmt) cc_final: 0.5094 (tmm) outliers start: 10 outliers final: 9 residues processed: 247 average time/residue: 0.5288 time to fit residues: 144.3410 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain 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 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 161 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.168339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120790 restraints weight = 15016.909| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.61 r_work: 0.3124 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15328 Z= 0.158 Angle : 0.562 10.267 20788 Z= 0.295 Chirality : 0.043 0.198 2348 Planarity : 0.003 0.024 2596 Dihedral : 6.930 59.434 2212 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.47 % Allowed : 14.59 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.19), residues: 1920 helix: 2.16 (0.14), residues: 1284 sheet: 0.25 (0.54), residues: 88 loop : -0.06 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 492 TYR 0.032 0.002 TYR A 411 PHE 0.013 0.002 PHE C 186 TRP 0.032 0.002 TRP C 281 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00362 (15328) covalent geometry : angle 0.56181 (20788) hydrogen bonds : bond 0.05007 ( 989) hydrogen bonds : angle 4.06058 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6237.30 seconds wall clock time: 106 minutes 30.97 seconds (6390.97 seconds total)