Starting phenix.real_space_refine on Thu Feb 5 03:24:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_44425.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_44425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_44425.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_44425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc6_44425/02_2026/9bc6_44425.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14972 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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 Time building chain proxies: 3.13, per 1000 atoms: 0.21 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: 1.24 Conformation dependent library (CDL) restraints added in 619.2 milliseconds 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: 0.50 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: 2.50 Time building geometry restraints manager: 1.63 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: 0.02 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- 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 are 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 : 0.460 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: 0.5739 time to fit residues: 205.3289 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 : 0.407 ------------------------------------------------------------------------------- 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 = 0.171007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122904 restraints weight = 14859.924| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.63 r_work: 0.3165 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1910 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= 0.141 Angle : 0.555 6.460 20788 Z= 0.303 Chirality : 0.043 0.155 2348 Planarity : 0.004 0.027 2596 Dihedral : 8.138 53.951 2236 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.27 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 are not related in a simple way. whole: 1.47 (0.19), residues: 1920 helix: 1.33 (0.14), residues: 1300 sheet: 0.45 (0.54), residues: 88 loop : 0.42 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 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 0.006 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00295 (15328) covalent geometry : angle 0.55542 (20788) hydrogen bonds : bond 0.05000 ( 989) hydrogen bonds : angle 4.31645 ( 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 : 0.457 Fit side-chains REVERT: A 195 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6612 (mmp-170) REVERT: A 257 VAL cc_start: 0.7572 (t) cc_final: 0.7186 (p) REVERT: A 283 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6708 (tp30) REVERT: A 287 MET cc_start: 0.4353 (ttp) cc_final: 0.3373 (tpt) REVERT: A 304 MET cc_start: 0.8667 (tpp) cc_final: 0.8404 (tpp) REVERT: A 343 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7933 (tptm) REVERT: A 408 GLN cc_start: 0.8249 (mm110) cc_final: 0.8040 (mm-40) REVERT: A 422 LYS cc_start: 0.8710 (mttp) cc_final: 0.8496 (mttt) REVERT: A 433 ASP cc_start: 0.8246 (t70) cc_final: 0.7993 (m-30) REVERT: A 459 GLU cc_start: 0.8392 (pt0) cc_final: 0.7991 (pp20) REVERT: A 483 PHE cc_start: 0.7117 (t80) cc_final: 0.6839 (t80) REVERT: B 195 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6583 (mmp-170) REVERT: B 257 VAL cc_start: 0.7565 (t) cc_final: 0.7179 (p) REVERT: B 283 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6705 (tp30) REVERT: B 287 MET cc_start: 0.4352 (ttp) cc_final: 0.3367 (tpt) REVERT: B 304 MET cc_start: 0.8673 (tpp) cc_final: 0.8408 (tpp) REVERT: B 343 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7922 (tptm) REVERT: B 408 GLN cc_start: 0.8244 (mm110) cc_final: 0.8040 (mm-40) REVERT: B 422 LYS cc_start: 0.8704 (mttp) cc_final: 0.8487 (mttt) REVERT: B 433 ASP cc_start: 0.8241 (t70) cc_final: 0.7987 (m-30) REVERT: B 459 GLU cc_start: 0.8380 (pt0) cc_final: 0.7916 (mt-10) REVERT: B 483 PHE cc_start: 0.7125 (t80) cc_final: 0.6845 (t80) REVERT: C 195 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6608 (mmp-170) REVERT: C 257 VAL cc_start: 0.7564 (t) cc_final: 0.7183 (p) REVERT: C 283 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6689 (tp30) REVERT: C 287 MET cc_start: 0.4355 (ttp) cc_final: 0.3366 (tpt) REVERT: C 304 MET cc_start: 0.8677 (tpp) cc_final: 0.8415 (tpp) REVERT: C 343 LYS cc_start: 0.8421 (mtmm) cc_final: 0.7927 (tptm) REVERT: C 408 GLN cc_start: 0.8235 (mm110) cc_final: 0.8034 (mm-40) REVERT: C 422 LYS cc_start: 0.8686 (mttp) cc_final: 0.8466 (mttt) REVERT: C 433 ASP cc_start: 0.8254 (t70) cc_final: 0.8007 (m-30) REVERT: C 459 GLU cc_start: 0.8392 (pt0) cc_final: 0.7938 (mt-10) REVERT: C 483 PHE cc_start: 0.7115 (t80) cc_final: 0.6786 (t80) REVERT: D 195 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6608 (mmp-170) REVERT: D 257 VAL cc_start: 0.7560 (t) cc_final: 0.7169 (p) REVERT: D 283 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6709 (tp30) REVERT: D 287 MET cc_start: 0.4363 (ttp) cc_final: 0.3374 (tpt) REVERT: D 304 MET cc_start: 0.8665 (tpp) cc_final: 0.8402 (tpp) REVERT: D 343 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7883 (tptt) REVERT: D 408 GLN cc_start: 0.8234 (mm110) cc_final: 0.8033 (mm-40) REVERT: D 422 LYS cc_start: 0.8684 (mttp) cc_final: 0.8465 (mttt) REVERT: D 433 ASP cc_start: 0.8250 (t70) cc_final: 0.8008 (m-30) REVERT: D 459 GLU cc_start: 0.8391 (pt0) cc_final: 0.7936 (mt-10) REVERT: D 483 PHE cc_start: 0.7111 (t80) cc_final: 0.6818 (t80) outliers start: 28 outliers final: 4 residues processed: 303 average time/residue: 0.5508 time to fit residues: 183.1053 Evaluate side-chains 268 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 0.4980 chunk 151 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.168141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120040 restraints weight = 14957.426| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15328 Z= 0.190 Angle : 0.587 6.662 20788 Z= 0.318 Chirality : 0.045 0.166 2348 Planarity : 0.004 0.032 2596 Dihedral : 8.335 55.854 2228 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.28 % Allowed : 8.94 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 1920 helix: 1.65 (0.14), residues: 1272 sheet: 0.55 (0.54), residues: 88 loop : 0.31 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 504 TYR 0.025 0.003 TYR D 347 PHE 0.019 0.002 PHE C 186 TRP 0.030 0.003 TRP B 281 HIS 0.004 0.002 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00445 (15328) covalent geometry : angle 0.58724 (20788) hydrogen bonds : bond 0.05661 ( 989) hydrogen bonds : angle 4.30521 ( 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 326 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 0.396 Fit side-chains REVERT: A 257 VAL cc_start: 0.7560 (t) cc_final: 0.7168 (p) REVERT: A 283 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6722 (tp30) REVERT: A 287 MET cc_start: 0.4722 (ttp) cc_final: 0.3789 (tpt) REVERT: A 343 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7919 (tptm) REVERT: A 433 ASP cc_start: 0.8327 (t70) cc_final: 0.7950 (m-30) REVERT: A 459 GLU cc_start: 0.8454 (pt0) cc_final: 0.7988 (mt-10) REVERT: A 483 PHE cc_start: 0.7049 (t80) cc_final: 0.6765 (t80) REVERT: B 208 LEU cc_start: 0.6794 (mt) cc_final: 0.6487 (mp) REVERT: B 257 VAL cc_start: 0.7556 (t) cc_final: 0.7161 (p) REVERT: B 283 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6702 (tp30) REVERT: B 287 MET cc_start: 0.4736 (ttp) cc_final: 0.3787 (tpt) REVERT: B 343 LYS cc_start: 0.8380 (mtmm) cc_final: 0.7918 (tptm) REVERT: B 433 ASP cc_start: 0.8331 (t70) cc_final: 0.7947 (m-30) REVERT: B 459 GLU cc_start: 0.8448 (pt0) cc_final: 0.7996 (mt-10) REVERT: B 483 PHE cc_start: 0.7062 (t80) cc_final: 0.6775 (t80) REVERT: C 208 LEU cc_start: 0.6796 (mt) cc_final: 0.6492 (mp) REVERT: C 257 VAL cc_start: 0.7551 (t) cc_final: 0.7165 (p) REVERT: C 283 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6731 (tp30) REVERT: C 287 MET cc_start: 0.4745 (ttp) cc_final: 0.3803 (tpt) REVERT: C 343 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7884 (tptm) REVERT: C 433 ASP cc_start: 0.8343 (t70) cc_final: 0.7949 (m-30) REVERT: C 459 GLU cc_start: 0.8448 (pt0) cc_final: 0.8003 (mt-10) REVERT: C 483 PHE cc_start: 0.7067 (t80) cc_final: 0.6787 (t80) REVERT: D 208 LEU cc_start: 0.6790 (mt) cc_final: 0.6482 (mp) REVERT: D 257 VAL cc_start: 0.7569 (t) cc_final: 0.7174 (p) REVERT: D 283 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6747 (tp30) REVERT: D 287 MET cc_start: 0.4732 (ttp) cc_final: 0.3790 (tpt) REVERT: D 343 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7871 (tptt) REVERT: D 433 ASP cc_start: 0.8343 (t70) cc_final: 0.7948 (m-30) REVERT: D 459 GLU cc_start: 0.8444 (pt0) cc_final: 0.7995 (mt-10) REVERT: D 483 PHE cc_start: 0.7060 (t80) cc_final: 0.6786 (t80) outliers start: 47 outliers final: 20 residues processed: 303 average time/residue: 0.5645 time to fit residues: 186.9446 Evaluate side-chains 261 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 180 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.169783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121798 restraints weight = 14902.386| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.62 r_work: 0.3142 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15328 Z= 0.129 Angle : 0.505 5.813 20788 Z= 0.272 Chirality : 0.041 0.163 2348 Planarity : 0.003 0.024 2596 Dihedral : 6.917 49.202 2212 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.30 % Allowed : 10.82 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 1920 helix: 1.88 (0.14), residues: 1276 sheet: 0.50 (0.54), residues: 88 loop : 0.31 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 504 TYR 0.018 0.002 TYR C 347 PHE 0.012 0.002 PHE D 389 TRP 0.026 0.002 TRP A 281 HIS 0.003 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00277 (15328) covalent geometry : angle 0.50468 (20788) hydrogen bonds : bond 0.04752 ( 989) hydrogen bonds : angle 4.10693 ( 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: 33 poor density : 264 time to evaluate : 0.606 Fit side-chains REVERT: A 257 VAL cc_start: 0.7521 (t) cc_final: 0.7122 (p) REVERT: A 283 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6691 (tp30) REVERT: A 287 MET cc_start: 0.4531 (ttp) cc_final: 0.3561 (tpt) REVERT: A 343 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7906 (tptm) REVERT: A 429 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7874 (tp40) REVERT: A 433 ASP cc_start: 0.8286 (t70) cc_final: 0.7991 (m-30) REVERT: A 459 GLU cc_start: 0.8386 (pt0) cc_final: 0.7959 (mt-10) REVERT: A 483 PHE cc_start: 0.7045 (t80) cc_final: 0.6764 (t80) REVERT: B 257 VAL cc_start: 0.7534 (t) cc_final: 0.7136 (p) REVERT: B 283 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6706 (tp30) REVERT: B 287 MET cc_start: 0.4541 (ttp) cc_final: 0.3564 (tpt) REVERT: B 343 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7905 (tptm) REVERT: B 433 ASP cc_start: 0.8281 (t70) cc_final: 0.7987 (m-30) REVERT: B 459 GLU cc_start: 0.8382 (pt0) cc_final: 0.7959 (mt-10) REVERT: B 483 PHE cc_start: 0.7046 (t80) cc_final: 0.6773 (t80) REVERT: C 257 VAL cc_start: 0.7530 (t) cc_final: 0.7129 (p) REVERT: C 283 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6708 (tp30) REVERT: C 287 MET cc_start: 0.4521 (ttp) cc_final: 0.3557 (tpt) REVERT: C 343 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7897 (tptm) REVERT: C 433 ASP cc_start: 0.8287 (t70) cc_final: 0.7979 (m-30) REVERT: C 459 GLU cc_start: 0.8379 (pt0) cc_final: 0.7959 (mt-10) REVERT: C 483 PHE cc_start: 0.7035 (t80) cc_final: 0.6749 (t80) REVERT: D 257 VAL cc_start: 0.7540 (t) cc_final: 0.7143 (p) REVERT: D 283 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6697 (tp30) REVERT: D 287 MET cc_start: 0.4535 (ttp) cc_final: 0.3551 (tpt) REVERT: D 343 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7850 (tptt) REVERT: D 433 ASP cc_start: 0.8290 (t70) cc_final: 0.7977 (m-30) REVERT: D 459 GLU cc_start: 0.8379 (pt0) cc_final: 0.7955 (mt-10) REVERT: D 483 PHE cc_start: 0.7050 (t80) cc_final: 0.6773 (t80) outliers start: 33 outliers final: 12 residues processed: 281 average time/residue: 0.5857 time to fit residues: 180.9232 Evaluate side-chains 253 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 133 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.169442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121507 restraints weight = 15040.469| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.62 r_work: 0.3135 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15328 Z= 0.140 Angle : 0.512 6.019 20788 Z= 0.275 Chirality : 0.042 0.172 2348 Planarity : 0.003 0.025 2596 Dihedral : 6.786 50.014 2212 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.75 % Allowed : 12.92 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1920 helix: 2.01 (0.14), residues: 1280 sheet: 0.39 (0.52), residues: 88 loop : 0.23 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 126 TYR 0.019 0.002 TYR D 347 PHE 0.012 0.002 PHE C 186 TRP 0.027 0.002 TRP C 281 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00313 (15328) covalent geometry : angle 0.51220 (20788) hydrogen bonds : bond 0.04832 ( 989) hydrogen bonds : angle 4.07078 ( 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 275 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 0.540 Fit side-chains REVERT: A 257 VAL cc_start: 0.7444 (t) cc_final: 0.7018 (p) REVERT: A 283 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6688 (tp30) REVERT: A 287 MET cc_start: 0.4551 (ttp) cc_final: 0.3558 (tpt) REVERT: A 343 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7883 (tptm) REVERT: A 433 ASP cc_start: 0.8292 (t70) cc_final: 0.7967 (m-30) REVERT: A 459 GLU cc_start: 0.8379 (pt0) cc_final: 0.7956 (mt-10) REVERT: A 483 PHE cc_start: 0.6963 (t80) cc_final: 0.6669 (t80) REVERT: B 257 VAL cc_start: 0.7446 (t) cc_final: 0.7020 (p) REVERT: B 283 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6687 (tp30) REVERT: B 287 MET cc_start: 0.4557 (ttp) cc_final: 0.3604 (tpt) REVERT: B 343 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7884 (tptm) REVERT: B 433 ASP cc_start: 0.8288 (t70) cc_final: 0.7967 (m-30) REVERT: B 459 GLU cc_start: 0.8372 (pt0) cc_final: 0.7965 (mt-10) REVERT: B 473 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5179 (tmm) REVERT: B 483 PHE cc_start: 0.6965 (t80) cc_final: 0.6670 (t80) REVERT: C 257 VAL cc_start: 0.7445 (t) cc_final: 0.7013 (p) REVERT: C 283 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6689 (tp30) REVERT: C 287 MET cc_start: 0.4558 (ttp) cc_final: 0.3617 (tpt) REVERT: C 343 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7887 (tptm) REVERT: C 433 ASP cc_start: 0.8291 (t70) cc_final: 0.7966 (m-30) REVERT: C 459 GLU cc_start: 0.8367 (pt0) cc_final: 0.7958 (mt-10) REVERT: C 473 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5264 (tmm) REVERT: C 483 PHE cc_start: 0.6954 (t80) cc_final: 0.6657 (t80) REVERT: D 257 VAL cc_start: 0.7448 (t) cc_final: 0.7022 (p) REVERT: D 283 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6683 (tp30) REVERT: D 287 MET cc_start: 0.4562 (ttp) cc_final: 0.3622 (tpt) REVERT: D 343 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7828 (tptt) REVERT: D 433 ASP cc_start: 0.8291 (t70) cc_final: 0.7962 (m-30) REVERT: D 459 GLU cc_start: 0.8369 (pt0) cc_final: 0.7954 (mt-10) REVERT: D 473 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5144 (tmm) REVERT: D 483 PHE cc_start: 0.6945 (t80) cc_final: 0.6652 (t80) outliers start: 25 outliers final: 11 residues processed: 267 average time/residue: 0.5858 time to fit residues: 171.6614 Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 370 SER Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 473 MET 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 473 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 178 optimal weight: 0.0370 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.166729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118946 restraints weight = 14890.265| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.61 r_work: 0.3099 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15328 Z= 0.229 Angle : 0.622 7.391 20788 Z= 0.334 Chirality : 0.046 0.181 2348 Planarity : 0.004 0.025 2596 Dihedral : 8.157 58.322 2212 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.86 % Allowed : 11.80 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 1920 helix: 1.75 (0.14), residues: 1280 sheet: 0.35 (0.54), residues: 88 loop : -0.01 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 126 TYR 0.025 0.003 TYR D 347 PHE 0.018 0.003 PHE B 186 TRP 0.031 0.003 TRP A 281 HIS 0.005 0.002 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00543 (15328) covalent geometry : angle 0.62194 (20788) hydrogen bonds : bond 0.05917 ( 989) hydrogen bonds : angle 4.29067 ( 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 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.421 Fit side-chains REVERT: A 187 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 257 VAL cc_start: 0.7486 (t) cc_final: 0.7060 (p) REVERT: A 283 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6734 (tp30) REVERT: A 287 MET cc_start: 0.4699 (ttp) cc_final: 0.3748 (tpt) REVERT: A 343 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7895 (tptm) REVERT: A 433 ASP cc_start: 0.8366 (t70) cc_final: 0.7959 (m-30) REVERT: A 459 GLU cc_start: 0.8374 (pt0) cc_final: 0.8000 (mt-10) REVERT: A 483 PHE cc_start: 0.6900 (t80) cc_final: 0.6673 (t80) REVERT: B 257 VAL cc_start: 0.7490 (t) cc_final: 0.7060 (p) REVERT: B 283 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6734 (tp30) REVERT: B 287 MET cc_start: 0.4711 (ttp) cc_final: 0.3747 (tpt) REVERT: B 343 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7893 (tptm) REVERT: B 433 ASP cc_start: 0.8371 (t70) cc_final: 0.7967 (m-30) REVERT: B 459 GLU cc_start: 0.8371 (pt0) cc_final: 0.8001 (mt-10) REVERT: B 473 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5310 (tmm) REVERT: B 483 PHE cc_start: 0.6894 (t80) cc_final: 0.6662 (t80) REVERT: C 187 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7297 (tt) REVERT: C 257 VAL cc_start: 0.7484 (t) cc_final: 0.7056 (p) REVERT: C 283 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6740 (tp30) REVERT: C 287 MET cc_start: 0.4707 (ttp) cc_final: 0.3758 (tpt) REVERT: C 343 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7874 (tptm) REVERT: C 433 ASP cc_start: 0.8375 (t70) cc_final: 0.7951 (m-30) REVERT: C 459 GLU cc_start: 0.8370 (pt0) cc_final: 0.7999 (mt-10) REVERT: C 473 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5313 (tmm) REVERT: C 483 PHE cc_start: 0.6902 (t80) cc_final: 0.6667 (t80) REVERT: D 187 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7296 (tt) REVERT: D 257 VAL cc_start: 0.7495 (t) cc_final: 0.7066 (p) REVERT: D 283 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6732 (tp30) REVERT: D 287 MET cc_start: 0.4700 (ttp) cc_final: 0.3750 (tpt) REVERT: D 433 ASP cc_start: 0.8365 (t70) cc_final: 0.7946 (m-30) REVERT: D 459 GLU cc_start: 0.8363 (pt0) cc_final: 0.7995 (mt-10) REVERT: D 473 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5303 (tmm) REVERT: D 483 PHE cc_start: 0.6900 (t80) cc_final: 0.6668 (t80) outliers start: 41 outliers final: 24 residues processed: 277 average time/residue: 0.5804 time to fit residues: 176.8618 Evaluate side-chains 271 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 A residue 494 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 523 ILE 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 473 MET Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.169882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122208 restraints weight = 14876.674| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.61 r_work: 0.3148 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15328 Z= 0.118 Angle : 0.491 5.689 20788 Z= 0.262 Chirality : 0.041 0.188 2348 Planarity : 0.003 0.022 2596 Dihedral : 6.794 55.921 2212 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.75 % Allowed : 13.55 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1920 helix: 2.08 (0.14), residues: 1284 sheet: 0.30 (0.53), residues: 88 loop : 0.21 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.021 0.002 TYR B 411 PHE 0.010 0.001 PHE C 389 TRP 0.029 0.002 TRP B 281 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00249 (15328) covalent geometry : angle 0.49116 (20788) hydrogen bonds : bond 0.04422 ( 989) hydrogen bonds : angle 4.00470 ( 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 266 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.455 Fit side-chains REVERT: A 257 VAL cc_start: 0.7355 (t) cc_final: 0.6897 (p) REVERT: A 283 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6700 (tp30) REVERT: A 287 MET cc_start: 0.4349 (ttp) cc_final: 0.3432 (tpt) REVERT: A 343 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7881 (tptm) REVERT: A 433 ASP cc_start: 0.8248 (t70) cc_final: 0.8006 (m-30) REVERT: A 459 GLU cc_start: 0.8336 (pt0) cc_final: 0.7968 (mt-10) REVERT: A 483 PHE cc_start: 0.6967 (t80) cc_final: 0.6740 (t80) REVERT: B 257 VAL cc_start: 0.7395 (t) cc_final: 0.6941 (p) REVERT: B 283 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6694 (tp30) REVERT: B 287 MET cc_start: 0.4347 (ttp) cc_final: 0.3422 (tpt) REVERT: B 343 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7884 (tptm) REVERT: B 433 ASP cc_start: 0.8241 (t70) cc_final: 0.8022 (m-30) REVERT: B 459 GLU cc_start: 0.8340 (pt0) cc_final: 0.7972 (mt-10) REVERT: B 473 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5262 (tmm) REVERT: B 483 PHE cc_start: 0.6963 (t80) cc_final: 0.6731 (t80) REVERT: C 257 VAL cc_start: 0.7380 (t) cc_final: 0.6922 (p) REVERT: C 283 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6700 (tp30) REVERT: C 287 MET cc_start: 0.4343 (ttp) cc_final: 0.3432 (tpt) REVERT: C 343 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7892 (tptm) REVERT: C 433 ASP cc_start: 0.8250 (t70) cc_final: 0.7994 (m-30) REVERT: C 459 GLU cc_start: 0.8339 (pt0) cc_final: 0.7974 (mt-10) REVERT: C 473 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5305 (tmm) REVERT: C 483 PHE cc_start: 0.6963 (t80) cc_final: 0.6729 (t80) REVERT: D 257 VAL cc_start: 0.7406 (t) cc_final: 0.6951 (p) REVERT: D 283 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6701 (tp30) REVERT: D 287 MET cc_start: 0.4354 (ttp) cc_final: 0.3435 (tpt) REVERT: D 433 ASP cc_start: 0.8247 (t70) cc_final: 0.7993 (m-30) REVERT: D 459 GLU cc_start: 0.8336 (pt0) cc_final: 0.7970 (mt-10) REVERT: D 473 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5226 (tmm) REVERT: D 483 PHE cc_start: 0.6964 (t80) cc_final: 0.6733 (t80) outliers start: 25 outliers final: 9 residues processed: 254 average time/residue: 0.5043 time to fit residues: 141.4700 Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 0.0670 chunk 111 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.172051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124657 restraints weight = 15114.702| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.62 r_work: 0.3175 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.102 Angle : 0.465 6.198 20788 Z= 0.245 Chirality : 0.040 0.187 2348 Planarity : 0.003 0.024 2596 Dihedral : 5.833 50.026 2212 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.82 % Allowed : 13.69 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.19), residues: 1920 helix: 2.32 (0.14), residues: 1288 sheet: 0.20 (0.52), residues: 88 loop : 0.48 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 504 TYR 0.026 0.001 TYR B 411 PHE 0.008 0.001 PHE C 514 TRP 0.024 0.002 TRP B 281 HIS 0.004 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00201 (15328) covalent geometry : angle 0.46451 (20788) hydrogen bonds : bond 0.03858 ( 989) hydrogen bonds : angle 3.81058 ( 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 275 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.403 Fit side-chains REVERT: A 257 VAL cc_start: 0.7294 (t) cc_final: 0.6835 (p) REVERT: A 283 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6651 (tp30) REVERT: A 287 MET cc_start: 0.4118 (ttp) cc_final: 0.3095 (tpt) REVERT: A 343 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7859 (tptm) REVERT: A 433 ASP cc_start: 0.8239 (t70) cc_final: 0.7998 (m-30) REVERT: A 459 GLU cc_start: 0.8327 (pt0) cc_final: 0.7968 (mt-10) REVERT: A 483 PHE cc_start: 0.7017 (t80) cc_final: 0.6806 (t80) REVERT: B 257 VAL cc_start: 0.7297 (t) cc_final: 0.6837 (p) REVERT: B 283 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6646 (tp30) REVERT: B 287 MET cc_start: 0.4125 (ttp) cc_final: 0.3098 (tpt) REVERT: B 343 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7866 (tptm) REVERT: B 429 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7884 (tp40) REVERT: B 459 GLU cc_start: 0.8327 (pt0) cc_final: 0.7964 (mt-10) REVERT: B 473 MET cc_start: 0.5848 (ttt) cc_final: 0.5313 (tmm) REVERT: B 483 PHE cc_start: 0.7006 (t80) cc_final: 0.6786 (t80) REVERT: C 257 VAL cc_start: 0.7308 (t) cc_final: 0.6839 (p) REVERT: C 283 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6656 (tp30) REVERT: C 287 MET cc_start: 0.4120 (ttp) cc_final: 0.3116 (tpt) REVERT: C 343 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7860 (tptm) REVERT: C 433 ASP cc_start: 0.8229 (t70) cc_final: 0.8011 (m-30) REVERT: C 459 GLU cc_start: 0.8321 (pt0) cc_final: 0.7968 (mt-10) REVERT: C 473 MET cc_start: 0.5870 (ttt) cc_final: 0.5329 (tmm) REVERT: C 483 PHE cc_start: 0.7021 (t80) cc_final: 0.6794 (t80) REVERT: D 218 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7431 (mt) REVERT: D 257 VAL cc_start: 0.7310 (t) cc_final: 0.6847 (p) REVERT: D 283 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6654 (tp30) REVERT: D 287 MET cc_start: 0.4132 (ttp) cc_final: 0.3106 (tpt) REVERT: D 343 LYS cc_start: 0.8461 (mtpp) cc_final: 0.7895 (tptt) REVERT: D 429 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7859 (tp40) REVERT: D 433 ASP cc_start: 0.8242 (t70) cc_final: 0.7984 (m-30) REVERT: D 459 GLU cc_start: 0.8323 (pt0) cc_final: 0.7965 (mt-10) REVERT: D 473 MET cc_start: 0.5866 (ttt) cc_final: 0.5333 (tmm) REVERT: D 483 PHE cc_start: 0.7021 (t80) cc_final: 0.6804 (t80) outliers start: 26 outliers final: 4 residues processed: 268 average time/residue: 0.5246 time to fit residues: 156.0289 Evaluate side-chains 240 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 235 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.171724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124078 restraints weight = 15065.573| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.62 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.105 Angle : 0.472 7.637 20788 Z= 0.249 Chirality : 0.040 0.191 2348 Planarity : 0.003 0.023 2596 Dihedral : 5.500 50.149 2204 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.70 % Allowed : 15.43 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.19), residues: 1920 helix: 2.38 (0.14), residues: 1288 sheet: 0.21 (0.52), residues: 88 loop : 0.52 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.029 0.001 TYR B 411 PHE 0.009 0.001 PHE C 389 TRP 0.025 0.002 TRP D 281 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00217 (15328) covalent geometry : angle 0.47201 (20788) hydrogen bonds : bond 0.04021 ( 989) hydrogen bonds : angle 3.77898 ( 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 246 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.472 Fit side-chains REVERT: A 257 VAL cc_start: 0.7273 (t) cc_final: 0.6814 (p) REVERT: A 283 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6605 (tp30) REVERT: A 285 PHE cc_start: 0.6847 (m-10) cc_final: 0.6595 (m-80) REVERT: A 287 MET cc_start: 0.4248 (ttp) cc_final: 0.3168 (tpt) REVERT: A 343 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7857 (tptm) REVERT: A 433 ASP cc_start: 0.8242 (t70) cc_final: 0.7985 (m-30) REVERT: A 459 GLU cc_start: 0.8322 (pt0) cc_final: 0.7956 (mt-10) REVERT: A 473 MET cc_start: 0.5796 (tmm) cc_final: 0.5241 (tmm) REVERT: B 257 VAL cc_start: 0.7273 (t) cc_final: 0.6808 (p) REVERT: B 283 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6616 (tp30) REVERT: B 285 PHE cc_start: 0.6855 (m-10) cc_final: 0.6601 (m-80) REVERT: B 287 MET cc_start: 0.4249 (ttp) cc_final: 0.3171 (tpt) REVERT: B 343 LYS cc_start: 0.8336 (mtmm) cc_final: 0.7854 (tptm) REVERT: B 429 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7849 (tp40) REVERT: B 459 GLU cc_start: 0.8325 (pt0) cc_final: 0.7963 (mt-10) REVERT: B 473 MET cc_start: 0.5833 (ttt) cc_final: 0.5246 (tmm) REVERT: C 257 VAL cc_start: 0.7268 (t) cc_final: 0.6795 (p) REVERT: C 283 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6575 (tp30) REVERT: C 287 MET cc_start: 0.4218 (ttp) cc_final: 0.3234 (tpt) REVERT: C 343 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7855 (tptm) REVERT: C 429 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7902 (tp40) REVERT: C 433 ASP cc_start: 0.8232 (t70) cc_final: 0.8006 (m-30) REVERT: C 459 GLU cc_start: 0.8328 (pt0) cc_final: 0.7961 (mt-10) REVERT: C 473 MET cc_start: 0.5827 (ttt) cc_final: 0.5240 (tmm) REVERT: D 257 VAL cc_start: 0.7276 (t) cc_final: 0.6808 (p) REVERT: D 283 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6606 (tp30) REVERT: D 285 PHE cc_start: 0.6847 (m-10) cc_final: 0.6596 (m-80) REVERT: D 287 MET cc_start: 0.4257 (ttp) cc_final: 0.3184 (tpt) REVERT: D 343 LYS cc_start: 0.8460 (mtpp) cc_final: 0.7904 (tptt) REVERT: D 429 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7872 (tp40) REVERT: D 433 ASP cc_start: 0.8198 (t70) cc_final: 0.7958 (m-30) REVERT: D 459 GLU cc_start: 0.8313 (pt0) cc_final: 0.7953 (mt-10) REVERT: D 473 MET cc_start: 0.5825 (ttt) cc_final: 0.5240 (tmm) outliers start: 10 outliers final: 0 residues processed: 242 average time/residue: 0.5643 time to fit residues: 149.8833 Evaluate side-chains 237 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.171552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123856 restraints weight = 15082.661| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.62 r_work: 0.3164 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15328 Z= 0.108 Angle : 0.479 8.972 20788 Z= 0.252 Chirality : 0.040 0.191 2348 Planarity : 0.003 0.023 2596 Dihedral : 5.438 49.828 2204 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.21 % Allowed : 15.50 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.19), residues: 1920 helix: 2.39 (0.14), residues: 1292 sheet: 0.19 (0.52), residues: 88 loop : 0.52 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 492 TYR 0.028 0.001 TYR B 411 PHE 0.011 0.001 PHE B 483 TRP 0.025 0.002 TRP C 281 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00223 (15328) covalent geometry : angle 0.47862 (20788) hydrogen bonds : bond 0.04082 ( 989) hydrogen bonds : angle 3.78449 ( 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 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.464 Fit side-chains REVERT: A 257 VAL cc_start: 0.7258 (t) cc_final: 0.6802 (p) REVERT: A 283 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6604 (tp30) REVERT: A 285 PHE cc_start: 0.6846 (m-10) cc_final: 0.6589 (m-80) REVERT: A 287 MET cc_start: 0.4177 (ttp) cc_final: 0.3223 (tpt) REVERT: A 343 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7851 (tptm) REVERT: A 459 GLU cc_start: 0.8328 (pt0) cc_final: 0.7963 (mt-10) REVERT: B 257 VAL cc_start: 0.7254 (t) cc_final: 0.6793 (p) REVERT: B 283 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6602 (tp30) REVERT: B 285 PHE cc_start: 0.6842 (m-10) cc_final: 0.6601 (m-80) REVERT: B 287 MET cc_start: 0.4179 (ttp) cc_final: 0.3227 (tpt) REVERT: B 343 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7846 (tptm) REVERT: B 459 GLU cc_start: 0.8328 (pt0) cc_final: 0.7965 (mt-10) REVERT: B 473 MET cc_start: 0.5773 (ttt) cc_final: 0.5195 (tmm) REVERT: C 257 VAL cc_start: 0.7251 (t) cc_final: 0.6787 (p) REVERT: C 283 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6592 (tp30) REVERT: C 285 PHE cc_start: 0.6844 (m-10) cc_final: 0.6586 (m-80) REVERT: C 287 MET cc_start: 0.4258 (ttp) cc_final: 0.3271 (tpt) REVERT: C 343 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7856 (tptm) REVERT: C 433 ASP cc_start: 0.8231 (t70) cc_final: 0.7990 (m-30) REVERT: C 459 GLU cc_start: 0.8328 (pt0) cc_final: 0.7967 (mt-10) REVERT: C 473 MET cc_start: 0.5731 (ttt) cc_final: 0.5238 (tmm) REVERT: D 257 VAL cc_start: 0.7255 (t) cc_final: 0.6794 (p) REVERT: D 283 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6598 (tp30) REVERT: D 285 PHE cc_start: 0.6849 (m-10) cc_final: 0.6590 (m-80) REVERT: D 287 MET cc_start: 0.4190 (ttp) cc_final: 0.3238 (tpt) REVERT: D 343 LYS cc_start: 0.8467 (mtpp) cc_final: 0.7898 (tptt) REVERT: D 429 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7890 (tp40) REVERT: D 433 ASP cc_start: 0.8209 (t70) cc_final: 0.7959 (m-30) REVERT: D 459 GLU cc_start: 0.8326 (pt0) cc_final: 0.7962 (mt-10) REVERT: D 473 MET cc_start: 0.5754 (ttt) cc_final: 0.5259 (tmm) outliers start: 3 outliers final: 1 residues processed: 243 average time/residue: 0.5580 time to fit residues: 149.0048 Evaluate side-chains 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 4.9990 chunk 182 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.168293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120544 restraints weight = 14978.149| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.59 r_work: 0.3117 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15328 Z= 0.171 Angle : 0.563 8.840 20788 Z= 0.300 Chirality : 0.043 0.198 2348 Planarity : 0.004 0.025 2596 Dihedral : 6.674 58.934 2204 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.70 % Allowed : 15.08 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1920 helix: 2.17 (0.14), residues: 1284 sheet: 0.20 (0.53), residues: 88 loop : 0.22 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 492 TYR 0.034 0.003 TYR B 411 PHE 0.015 0.002 PHE C 186 TRP 0.030 0.002 TRP B 281 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00397 (15328) covalent geometry : angle 0.56295 (20788) hydrogen bonds : bond 0.05231 ( 989) hydrogen bonds : angle 4.04268 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6400.06 seconds wall clock time: 109 minutes 25.53 seconds (6565.53 seconds total)