Starting phenix.real_space_refine on Fri Sep 19 01:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.map" model { file = "/net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev7_19993/09_2025/9ev7_19993.cif" } resolution = 2.74 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= 0.002 sd= 0.035 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 52 5.16 5 C 14303 2.51 5 N 3641 2.21 5 O 4199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4688 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4641 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3471 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4705 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4690 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 5.70, per 1000 atoms: 0.26 Number of scatterers: 22195 At special positions: 0 Unit cell: (139.656, 146.427, 157.43, 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 52 16.00 O 4199 8.00 N 3641 7.00 C 14303 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 28 sheets defined 29.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.942A pdb=" N SER A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.864A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.838A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.708A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.983A pdb=" N SER B 314 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.769A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.508A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 605 through 636 Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.102A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.835A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.827A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.511A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.925A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.099A pdb=" N SER D 314 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.865A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.844A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.503A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.710A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.062A pdb=" N SER E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.800A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.517A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 605 through 637 Proline residue: E 621 - end of helix removed outlier: 3.921A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.994A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.226A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.323A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.319A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.085A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.193A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.426A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.313A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.067A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 212 removed outlier: 4.269A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.245A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.198A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.039A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.110A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.521A pdb=" N ASP D 287 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.278A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.125A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.684A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.330A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.448A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.229A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 397 through 399 removed outlier: 4.964A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4656 1.33 - 1.45: 5390 1.45 - 1.57: 12589 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 22709 Sorted by residual: bond pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.62e+01 bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.61e+01 bond pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.59e+01 bond pdb=" CA GLU B 103 " pdb=" C GLU B 103 " ideal model delta sigma weight residual 1.526 1.490 0.037 9.20e-03 1.18e+04 1.58e+01 ... (remaining 22704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 30423 1.75 - 3.50: 428 3.50 - 5.25: 55 5.25 - 7.01: 18 7.01 - 8.76: 13 Bond angle restraints: 30937 Sorted by residual: angle pdb=" N TYR B 620 " pdb=" CA TYR B 620 " pdb=" C TYR B 620 " ideal model delta sigma weight residual 113.25 119.40 -6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" N GLU D 103 " pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 110.56 101.80 8.76 1.94e+00 2.66e-01 2.04e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.88 8.68 1.94e+00 2.66e-01 2.00e+01 angle pdb=" N GLU B 103 " pdb=" CA GLU B 103 " pdb=" C GLU B 103 " ideal model delta sigma weight residual 110.56 101.88 8.68 1.94e+00 2.66e-01 2.00e+01 ... (remaining 30932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 12716 14.37 - 28.74: 445 28.74 - 43.12: 139 43.12 - 57.49: 22 57.49 - 71.86: 10 Dihedral angle restraints: 13332 sinusoidal: 5160 harmonic: 8172 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE E 522 " pdb=" C ILE E 522 " pdb=" N PHE E 523 " pdb=" CA PHE E 523 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2970 0.056 - 0.112: 464 0.112 - 0.168: 84 0.168 - 0.224: 1 0.224 - 0.279: 9 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 620 " pdb=" N TYR A 620 " pdb=" C TYR A 620 " pdb=" CB TYR A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3525 not shown) Planarity restraints: 4019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 197 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C LEU B 197 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 197 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU B 198 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 200 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO B 201 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 199 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C ILE D 199 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE D 199 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 200 " 0.015 2.00e-02 2.50e+03 ... (remaining 4016 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1465 2.74 - 3.28: 20634 3.28 - 3.82: 34427 3.82 - 4.36: 40215 4.36 - 4.90: 72656 Nonbonded interactions: 169397 Sorted by model distance: nonbonded pdb=" OG SER E 367 " pdb=" OD1 ASP E 369 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.243 3.040 nonbonded pdb=" CB HIS B 222 " pdb=" CD1 LEU B 325 " model vdw 2.246 3.860 ... (remaining 169392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 123 or (resid 124 and (name N or n \ ame CA or name C or name O or name CB )) or resid 125 through 195 or (resid 196 \ through 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 or (resid 202 through 203 and (name N or name CA or name C or name O or name C \ B )) or resid 204 through 205 or (resid 206 through 208 and (name N or name CA o \ r name C or name O or name CB )) or resid 209 through 240 or (resid 241 through \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throug \ h 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 292 or (resid 293 and (name N or name CA or name C or name O o \ r name CB )) or resid 294 through 311 or (resid 312 through 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 or (resid \ 321 through 322 and (name N or name CA or name C or name O or name CB )) or resi \ d 323 through 637)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 or (resid 107 and (name N \ or name CA or name C or name O or name CB )) or resid 108 through 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB )) or resid 125 throug \ h 637)) selection = (chain 'D' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB )) or resid 125 through 195 or (resid 196 through 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 or (resid 202 through 203 and (n \ ame N or name CA or name C or name O or name CB )) or resid 204 through 205 or ( \ resid 206 through 208 and (name N or name CA or name C or name O or name CB )) o \ r resid 209 through 240 or (resid 241 through 242 and (name N or name CA or name \ C or name O or name CB )) or resid 243 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 289 or (resid 29 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 291 or (resi \ d 292 through 293 and (name N or name CA or name C or name O or name CB )) or re \ sid 294 through 311 or (resid 312 through 313 and (name N or name CA or name C o \ r name O or name CB )) or resid 314 through 318 or (resid 319 and (name N or nam \ e CA or name C or name O or name CB )) or resid 320 or (resid 321 through 322 an \ d (name N or name CA or name C or name O or name CB )) or resid 323 through 637) \ ) selection = (chain 'E' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 195 or (resid 196 through 200 and (name N or name CA or name C or na \ me O or name CB )) or resid 201 through 205 or (resid 206 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 through 240 or (resi \ d 241 through 242 and (name N or name CA or name C or name O or name CB )) or re \ sid 243 through 263 or (resid 264 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 291 or (resid 292 through 293 and (name N or nam \ e CA or name C or name O or name CB )) or resid 294 through 311 or (resid 312 th \ rough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 320 or (resid 321 through 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 637)) } 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.350 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.003 0.052 22709 Z= 0.217 Angle : 0.552 8.758 30937 Z= 0.315 Chirality : 0.044 0.279 3528 Planarity : 0.004 0.064 4019 Dihedral : 8.721 71.862 8094 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 0.58 % Allowed : 3.11 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 2830 helix: 1.93 (0.21), residues: 677 sheet: 0.91 (0.16), residues: 959 loop : -0.33 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 599 TYR 0.008 0.001 TYR B 517 PHE 0.011 0.001 PHE A 561 TRP 0.005 0.001 TRP D 534 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00315 (22709) covalent geometry : angle 0.55226 (30937) hydrogen bonds : bond 0.19264 ( 1045) hydrogen bonds : angle 6.36311 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 580 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8489 (mt0) cc_final: 0.8261 (mt0) REVERT: A 414 PHE cc_start: 0.7611 (p90) cc_final: 0.7205 (p90) REVERT: A 597 GLN cc_start: 0.8131 (mt0) cc_final: 0.7919 (mt0) REVERT: A 632 TYR cc_start: 0.8339 (t80) cc_final: 0.8129 (t80) REVERT: B 249 LEU cc_start: 0.8411 (tp) cc_final: 0.8201 (tt) REVERT: B 354 THR cc_start: 0.8578 (m) cc_final: 0.8376 (p) REVERT: C 206 GLN cc_start: 0.6854 (tt0) cc_final: 0.6607 (tt0) REVERT: C 400 TYR cc_start: 0.8072 (t80) cc_final: 0.7707 (t80) REVERT: C 444 ASP cc_start: 0.8047 (p0) cc_final: 0.7804 (p0) REVERT: C 458 THR cc_start: 0.8287 (t) cc_final: 0.7907 (m) REVERT: C 487 TYR cc_start: 0.8258 (p90) cc_final: 0.7926 (p90) REVERT: C 517 TYR cc_start: 0.8378 (t80) cc_final: 0.8161 (t80) REVERT: D 517 TYR cc_start: 0.8422 (t80) cc_final: 0.8149 (t80) REVERT: D 560 ASN cc_start: 0.7884 (t0) cc_final: 0.7670 (t0) REVERT: E 277 GLN cc_start: 0.7399 (mp10) cc_final: 0.6771 (mp-120) REVERT: E 304 VAL cc_start: 0.8198 (p) cc_final: 0.7976 (m) REVERT: E 354 THR cc_start: 0.8334 (m) cc_final: 0.8121 (p) REVERT: E 411 GLN cc_start: 0.8213 (tt0) cc_final: 0.7988 (tt0) REVERT: E 599 ARG cc_start: 0.8417 (tpt170) cc_final: 0.8188 (tpt170) outliers start: 14 outliers final: 3 residues processed: 590 average time/residue: 0.6912 time to fit residues: 460.5395 Evaluate side-chains 500 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 497 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 255 LYS Chi-restraints excluded: chain E residue 328 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 221 GLN A 611 GLN B 233 HIS B 307 ASN B 410 ASN B 411 GLN C 307 ASN C 344 GLN D 221 GLN D 409 GLN D 411 GLN E 338 GLN E 344 GLN E 360 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130405 restraints weight = 32683.235| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.40 r_work: 0.3513 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 22709 Z= 0.312 Angle : 0.697 8.282 30937 Z= 0.377 Chirality : 0.051 0.195 3528 Planarity : 0.005 0.046 4019 Dihedral : 5.049 45.756 3072 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.57 % Allowed : 10.71 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2830 helix: 1.69 (0.20), residues: 718 sheet: 0.93 (0.16), residues: 943 loop : -0.54 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 504 TYR 0.028 0.003 TYR B 53 PHE 0.025 0.003 PHE B 135 TRP 0.017 0.002 TRP A 359 HIS 0.009 0.002 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00756 (22709) covalent geometry : angle 0.69676 (30937) hydrogen bonds : bond 0.08630 ( 1045) hydrogen bonds : angle 5.18710 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 516 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4985 (mtm) REVERT: A 340 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8401 (t) REVERT: A 414 PHE cc_start: 0.8305 (p90) cc_final: 0.7886 (p90) REVERT: A 521 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7958 (mmm-85) REVERT: A 599 ARG cc_start: 0.8773 (tpt170) cc_final: 0.8499 (tpt170) REVERT: B 405 ASN cc_start: 0.8354 (m110) cc_final: 0.8102 (m-40) REVERT: B 620 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: C 414 PHE cc_start: 0.8263 (p90) cc_final: 0.8028 (p90) REVERT: C 458 THR cc_start: 0.8493 (t) cc_final: 0.8204 (m) REVERT: C 473 VAL cc_start: 0.8421 (m) cc_final: 0.8207 (t) REVERT: C 620 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: C 622 LEU cc_start: 0.8152 (tp) cc_final: 0.7942 (tp) REVERT: D 122 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6194 (p0) REVERT: D 327 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7573 (t) REVERT: D 515 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8387 (mp) REVERT: E 277 GLN cc_start: 0.7853 (mp10) cc_final: 0.7616 (mp-120) REVERT: E 403 GLN cc_start: 0.7893 (tp40) cc_final: 0.7416 (tp-100) REVERT: E 480 GLU cc_start: 0.7638 (mp0) cc_final: 0.7276 (mp0) outliers start: 62 outliers final: 25 residues processed: 542 average time/residue: 0.6880 time to fit residues: 418.0538 Evaluate side-chains 506 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 474 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 439 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 206 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 233 HIS A 432 GLN A 611 GLN B 348 ASN B 360 HIS ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN C 502 ASN C 560 ASN D 348 ASN D 432 GLN E 221 GLN E 338 GLN E 411 GLN E 560 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136483 restraints weight = 32642.337| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.39 r_work: 0.3585 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22709 Z= 0.111 Angle : 0.524 8.146 30937 Z= 0.275 Chirality : 0.043 0.155 3528 Planarity : 0.004 0.045 4019 Dihedral : 4.500 34.782 3066 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.53 % Allowed : 14.08 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2830 helix: 2.15 (0.21), residues: 724 sheet: 1.04 (0.16), residues: 987 loop : -0.47 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 521 TYR 0.017 0.001 TYR A 300 PHE 0.026 0.001 PHE A 561 TRP 0.010 0.001 TRP A 359 HIS 0.004 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00228 (22709) covalent geometry : angle 0.52371 (30937) hydrogen bonds : bond 0.05071 ( 1045) hydrogen bonds : angle 4.56523 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 478 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.8259 (p90) cc_final: 0.7844 (p90) REVERT: A 521 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7888 (mmm-85) REVERT: A 599 ARG cc_start: 0.8520 (tpt170) cc_final: 0.8234 (tpt170) REVERT: B 340 VAL cc_start: 0.8884 (m) cc_final: 0.8657 (p) REVERT: B 515 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 560 ASN cc_start: 0.8269 (t0) cc_final: 0.8066 (t0) REVERT: B 620 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: C 403 GLN cc_start: 0.7771 (tp40) cc_final: 0.7565 (mm-40) REVERT: C 414 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7679 (p90) REVERT: C 473 VAL cc_start: 0.8372 (m) cc_final: 0.8144 (t) REVERT: C 552 ASN cc_start: 0.8617 (t0) cc_final: 0.8387 (t0) REVERT: C 620 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: D 163 TYR cc_start: 0.7946 (m-80) cc_final: 0.7518 (m-80) REVERT: D 230 ASP cc_start: 0.7288 (m-30) cc_final: 0.7070 (m-30) REVERT: D 327 SER cc_start: 0.7914 (p) cc_final: 0.7562 (t) REVERT: D 414 PHE cc_start: 0.8444 (p90) cc_final: 0.8101 (p90) REVERT: D 515 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (mp) REVERT: E 303 LEU cc_start: 0.7659 (tp) cc_final: 0.7455 (tp) REVERT: E 480 GLU cc_start: 0.7571 (mp0) cc_final: 0.7205 (mp0) outliers start: 61 outliers final: 22 residues processed: 507 average time/residue: 0.6651 time to fit residues: 378.9311 Evaluate side-chains 493 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 466 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 160 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS A 611 GLN B 360 HIS B 405 ASN B 432 GLN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN C 502 ASN C 514 ASN E 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.158347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130904 restraints weight = 32907.306| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.34 r_work: 0.3496 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 22709 Z= 0.300 Angle : 0.681 8.805 30937 Z= 0.363 Chirality : 0.050 0.173 3528 Planarity : 0.005 0.054 4019 Dihedral : 5.021 36.970 3066 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.78 % Allowed : 14.33 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2830 helix: 1.90 (0.20), residues: 706 sheet: 0.90 (0.16), residues: 952 loop : -0.74 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 155 TYR 0.026 0.002 TYR D 53 PHE 0.033 0.003 PHE B 414 TRP 0.028 0.002 TRP D 121 HIS 0.011 0.002 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00731 (22709) covalent geometry : angle 0.68139 (30937) hydrogen bonds : bond 0.08383 ( 1045) hydrogen bonds : angle 5.11933 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 508 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6503 (ptm) cc_final: 0.6177 (ptm) REVERT: A 224 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: A 340 VAL cc_start: 0.8778 (m) cc_final: 0.8422 (t) REVERT: A 414 PHE cc_start: 0.8302 (p90) cc_final: 0.7863 (p90) REVERT: A 521 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7967 (mmm-85) REVERT: A 599 ARG cc_start: 0.8774 (tpt170) cc_final: 0.8559 (tpt170) REVERT: B 323 VAL cc_start: 0.8442 (t) cc_final: 0.8129 (m) REVERT: B 620 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: C 270 GLU cc_start: 0.7686 (pt0) cc_final: 0.7448 (pt0) REVERT: C 374 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8121 (m) REVERT: C 403 GLN cc_start: 0.7931 (tp40) cc_final: 0.7689 (mm-40) REVERT: C 414 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7595 (p90) REVERT: C 449 SER cc_start: 0.8768 (p) cc_final: 0.8560 (t) REVERT: C 481 GLU cc_start: 0.8018 (tt0) cc_final: 0.7761 (tt0) REVERT: C 620 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: C 622 LEU cc_start: 0.8242 (tp) cc_final: 0.7981 (tp) REVERT: D 82 MET cc_start: 0.3970 (mmm) cc_final: 0.3750 (mmm) REVERT: D 122 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6276 (t70) REVERT: D 163 TYR cc_start: 0.8130 (m-80) cc_final: 0.7703 (m-80) REVERT: D 327 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7669 (t) REVERT: D 498 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5881 (tpp-160) REVERT: D 515 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8420 (mp) REVERT: E 303 LEU cc_start: 0.7753 (tp) cc_final: 0.7516 (tp) REVERT: E 354 THR cc_start: 0.8747 (m) cc_final: 0.8547 (p) REVERT: E 480 GLU cc_start: 0.7612 (mp0) cc_final: 0.7286 (mp0) outliers start: 91 outliers final: 41 residues processed: 558 average time/residue: 0.7261 time to fit residues: 455.6400 Evaluate side-chains 554 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 504 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 25 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN A 446 GLN B 405 ASN B 560 ASN C 307 ASN C 410 ASN C 432 GLN C 502 ASN C 514 ASN C 560 ASN D 153 ASN E 144 HIS E 206 GLN E 277 GLN E 560 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.160345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132364 restraints weight = 32142.572| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.37 r_work: 0.3523 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22709 Z= 0.196 Angle : 0.600 8.558 30937 Z= 0.318 Chirality : 0.046 0.220 3528 Planarity : 0.005 0.047 4019 Dihedral : 4.837 35.866 3066 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.61 % Allowed : 15.49 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2830 helix: 2.06 (0.20), residues: 706 sheet: 0.85 (0.16), residues: 949 loop : -0.70 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 420 TYR 0.026 0.002 TYR B 143 PHE 0.055 0.002 PHE A 561 TRP 0.016 0.002 TRP D 121 HIS 0.006 0.001 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00467 (22709) covalent geometry : angle 0.60011 (30937) hydrogen bonds : bond 0.06726 ( 1045) hydrogen bonds : angle 4.87418 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 497 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7559 (tt) REVERT: A 82 MET cc_start: 0.6604 (ptm) cc_final: 0.6243 (ptm) REVERT: A 224 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: A 340 VAL cc_start: 0.8750 (m) cc_final: 0.8392 (t) REVERT: A 414 PHE cc_start: 0.8276 (p90) cc_final: 0.7877 (p90) REVERT: A 521 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7964 (mtp85) REVERT: A 599 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8408 (tpt170) REVERT: A 613 ASP cc_start: 0.7948 (m-30) cc_final: 0.7741 (m-30) REVERT: B 109 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 323 VAL cc_start: 0.8494 (t) cc_final: 0.8193 (m) REVERT: B 340 VAL cc_start: 0.8925 (p) cc_final: 0.8672 (t) REVERT: B 580 MET cc_start: 0.8301 (mmm) cc_final: 0.7846 (mmm) REVERT: B 620 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: C 270 GLU cc_start: 0.7627 (pt0) cc_final: 0.7393 (pt0) REVERT: C 403 GLN cc_start: 0.7906 (tp40) cc_final: 0.7614 (mm-40) REVERT: C 414 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7554 (p90) REVERT: C 481 GLU cc_start: 0.8006 (tt0) cc_final: 0.7753 (tt0) REVERT: C 498 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.5389 (tpp-160) REVERT: C 620 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: D 82 MET cc_start: 0.4260 (mmm) cc_final: 0.4038 (mmt) REVERT: D 163 TYR cc_start: 0.8131 (m-80) cc_final: 0.7787 (m-80) REVERT: D 230 ASP cc_start: 0.7312 (m-30) cc_final: 0.7107 (m-30) REVERT: D 327 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (t) REVERT: D 345 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7766 (mtp85) REVERT: D 414 PHE cc_start: 0.8451 (p90) cc_final: 0.8107 (p90) REVERT: D 481 GLU cc_start: 0.7954 (tt0) cc_final: 0.7732 (tt0) REVERT: D 498 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5898 (tpp-160) REVERT: D 515 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8378 (mp) REVERT: E 155 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7394 (mtp85) REVERT: E 247 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7048 (tp) REVERT: E 480 GLU cc_start: 0.7636 (mp0) cc_final: 0.7312 (mp0) REVERT: E 620 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7400 (m-80) outliers start: 87 outliers final: 48 residues processed: 541 average time/residue: 0.7591 time to fit residues: 459.6624 Evaluate side-chains 551 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 491 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 162 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 222 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS A 611 GLN B 405 ASN C 410 ASN C 502 ASN C 560 ASN D 560 ASN E 206 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133914 restraints weight = 32252.889| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.37 r_work: 0.3543 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22709 Z= 0.144 Angle : 0.555 8.894 30937 Z= 0.293 Chirality : 0.044 0.173 3528 Planarity : 0.004 0.045 4019 Dihedral : 4.634 33.354 3066 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 16.40 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 2830 helix: 2.30 (0.21), residues: 700 sheet: 0.90 (0.16), residues: 953 loop : -0.64 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.020 0.002 TYR B 143 PHE 0.051 0.002 PHE A 561 TRP 0.012 0.001 TRP A 359 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00329 (22709) covalent geometry : angle 0.55508 (30937) hydrogen bonds : bond 0.05821 ( 1045) hydrogen bonds : angle 4.68472 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 482 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6718 (ptm) cc_final: 0.6342 (ptm) REVERT: A 199 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4715 (mp) REVERT: A 224 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7863 (ttp80) REVERT: A 340 VAL cc_start: 0.8734 (m) cc_final: 0.8346 (t) REVERT: A 414 PHE cc_start: 0.8274 (p90) cc_final: 0.7882 (p90) REVERT: A 521 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7953 (mmm-85) REVERT: A 599 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8333 (tpt170) REVERT: B 323 VAL cc_start: 0.8495 (t) cc_final: 0.8207 (m) REVERT: B 340 VAL cc_start: 0.8848 (p) cc_final: 0.8597 (t) REVERT: B 473 VAL cc_start: 0.8466 (m) cc_final: 0.8252 (t) REVERT: B 515 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 560 ASN cc_start: 0.8213 (t0) cc_final: 0.7965 (t0) REVERT: B 620 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: C 270 GLU cc_start: 0.7635 (pt0) cc_final: 0.7391 (pt0) REVERT: C 414 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7625 (p90) REVERT: C 425 GLU cc_start: 0.8324 (tt0) cc_final: 0.8039 (tt0) REVERT: C 498 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.5367 (tpp-160) REVERT: C 620 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: C 622 LEU cc_start: 0.8122 (tp) cc_final: 0.7795 (tp) REVERT: D 122 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6213 (t70) REVERT: D 163 TYR cc_start: 0.8146 (m-80) cc_final: 0.7812 (m-80) REVERT: D 230 ASP cc_start: 0.7303 (m-30) cc_final: 0.7072 (m-30) REVERT: D 345 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7756 (mtp85) REVERT: D 414 PHE cc_start: 0.8446 (p90) cc_final: 0.8240 (p90) REVERT: D 498 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5860 (tpp-160) REVERT: D 515 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (mp) REVERT: E 155 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7369 (mtp85) REVERT: E 432 GLN cc_start: 0.8000 (mt0) cc_final: 0.7789 (mt0) REVERT: E 480 GLU cc_start: 0.7632 (mp0) cc_final: 0.7281 (mp0) REVERT: E 544 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7759 (ttm-80) REVERT: E 620 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.7324 (m-80) outliers start: 70 outliers final: 41 residues processed: 516 average time/residue: 0.7734 time to fit residues: 445.4294 Evaluate side-chains 529 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 476 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 147 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 231 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN A 611 GLN B 405 ASN C 410 ASN C 502 ASN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131472 restraints weight = 32503.398| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.43 r_work: 0.3534 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22709 Z= 0.165 Angle : 0.572 9.306 30937 Z= 0.301 Chirality : 0.044 0.164 3528 Planarity : 0.004 0.047 4019 Dihedral : 4.648 31.294 3066 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.20 % Allowed : 16.45 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 2830 helix: 2.27 (0.20), residues: 700 sheet: 0.88 (0.16), residues: 943 loop : -0.67 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 420 TYR 0.017 0.002 TYR B 143 PHE 0.046 0.002 PHE A 561 TRP 0.014 0.001 TRP B 121 HIS 0.005 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00386 (22709) covalent geometry : angle 0.57187 (30937) hydrogen bonds : bond 0.06085 ( 1045) hydrogen bonds : angle 4.69185 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 474 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6793 (ptm) cc_final: 0.6408 (ptm) REVERT: A 199 ILE cc_start: 0.4975 (OUTLIER) cc_final: 0.4587 (mp) REVERT: A 224 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: A 340 VAL cc_start: 0.8739 (m) cc_final: 0.8347 (t) REVERT: A 414 PHE cc_start: 0.8300 (p90) cc_final: 0.7872 (p90) REVERT: A 521 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: A 599 ARG cc_start: 0.8605 (tpt170) cc_final: 0.8201 (tpt170) REVERT: B 323 VAL cc_start: 0.8510 (t) cc_final: 0.8243 (m) REVERT: B 340 VAL cc_start: 0.8828 (p) cc_final: 0.8589 (t) REVERT: B 620 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: C 270 GLU cc_start: 0.7641 (pt0) cc_final: 0.7367 (pt0) REVERT: C 414 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7525 (p90) REVERT: C 425 GLU cc_start: 0.8327 (tt0) cc_final: 0.8111 (tt0) REVERT: C 481 GLU cc_start: 0.7994 (tt0) cc_final: 0.7739 (tt0) REVERT: C 498 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5327 (tpp-160) REVERT: C 620 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: C 622 LEU cc_start: 0.8129 (tp) cc_final: 0.7793 (tp) REVERT: D 122 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6260 (t70) REVERT: D 163 TYR cc_start: 0.8144 (m-80) cc_final: 0.7862 (m-80) REVERT: D 230 ASP cc_start: 0.7251 (m-30) cc_final: 0.7028 (m-30) REVERT: D 345 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7803 (mtp85) REVERT: D 414 PHE cc_start: 0.8473 (p90) cc_final: 0.8190 (p90) REVERT: D 515 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8367 (mp) REVERT: E 155 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7310 (mtp85) REVERT: E 247 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6858 (tt) REVERT: E 480 GLU cc_start: 0.7628 (mp0) cc_final: 0.7274 (mp0) REVERT: E 544 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7741 (ttm-80) REVERT: E 599 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8375 (tmt170) REVERT: E 620 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7374 (m-80) outliers start: 77 outliers final: 49 residues processed: 512 average time/residue: 0.7687 time to fit residues: 440.0134 Evaluate side-chains 535 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 475 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 26 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 206 optimal weight: 0.0070 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 611 GLN B 405 ASN C 403 GLN C 410 ASN C 502 ASN C 560 ASN D 432 GLN D 560 ASN E 338 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132424 restraints weight = 32635.023| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.47 r_work: 0.3540 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22709 Z= 0.141 Angle : 0.551 9.370 30937 Z= 0.289 Chirality : 0.043 0.159 3528 Planarity : 0.004 0.045 4019 Dihedral : 4.547 27.346 3066 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.03 % Allowed : 16.40 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 2830 helix: 2.31 (0.20), residues: 706 sheet: 0.84 (0.16), residues: 959 loop : -0.62 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 420 TYR 0.023 0.002 TYR B 65 PHE 0.043 0.002 PHE A 561 TRP 0.018 0.001 TRP B 121 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00324 (22709) covalent geometry : angle 0.55130 (30937) hydrogen bonds : bond 0.05560 ( 1045) hydrogen bonds : angle 4.60378 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 459 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6802 (ptm) cc_final: 0.6396 (ptm) REVERT: A 199 ILE cc_start: 0.5090 (OUTLIER) cc_final: 0.4677 (mp) REVERT: A 224 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: A 340 VAL cc_start: 0.8739 (m) cc_final: 0.8351 (t) REVERT: A 414 PHE cc_start: 0.8293 (p90) cc_final: 0.7877 (p90) REVERT: A 521 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: A 599 ARG cc_start: 0.8551 (tpt170) cc_final: 0.8142 (tpt170) REVERT: B 323 VAL cc_start: 0.8533 (t) cc_final: 0.8278 (m) REVERT: B 340 VAL cc_start: 0.8775 (p) cc_final: 0.8522 (t) REVERT: B 515 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 620 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: C 270 GLU cc_start: 0.7591 (pt0) cc_final: 0.7332 (pt0) REVERT: C 277 GLN cc_start: 0.8203 (mp10) cc_final: 0.7786 (mp10) REVERT: C 403 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: C 414 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7497 (p90) REVERT: C 425 GLU cc_start: 0.8318 (tt0) cc_final: 0.8034 (tt0) REVERT: C 498 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5402 (tpp-160) REVERT: C 620 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: D 122 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6264 (t70) REVERT: D 163 TYR cc_start: 0.8110 (m-80) cc_final: 0.7824 (m-80) REVERT: D 230 ASP cc_start: 0.7320 (m-30) cc_final: 0.7058 (m-30) REVERT: D 345 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7799 (mtp85) REVERT: D 414 PHE cc_start: 0.8480 (p90) cc_final: 0.8186 (p90) REVERT: D 515 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8356 (mp) REVERT: E 168 PHE cc_start: 0.6953 (p90) cc_final: 0.6496 (p90) REVERT: E 480 GLU cc_start: 0.7611 (mp0) cc_final: 0.7238 (mp0) REVERT: E 544 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7707 (ttm-80) REVERT: E 599 ARG cc_start: 0.8558 (tpt90) cc_final: 0.8253 (tmt170) REVERT: E 620 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7364 (m-80) outliers start: 73 outliers final: 47 residues processed: 493 average time/residue: 0.7812 time to fit residues: 430.1970 Evaluate side-chains 514 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 456 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 23 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 68 optimal weight: 0.0050 chunk 143 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN B 405 ASN C 403 GLN C 410 ASN C 502 ASN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.161195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132523 restraints weight = 32768.662| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.47 r_work: 0.3542 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22709 Z= 0.139 Angle : 0.559 12.062 30937 Z= 0.292 Chirality : 0.043 0.159 3528 Planarity : 0.004 0.045 4019 Dihedral : 4.478 21.985 3064 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.07 % Allowed : 16.82 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2830 helix: 2.31 (0.20), residues: 706 sheet: 0.83 (0.16), residues: 959 loop : -0.59 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 155 TYR 0.021 0.002 TYR B 65 PHE 0.042 0.002 PHE A 561 TRP 0.032 0.001 TRP B 121 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00319 (22709) covalent geometry : angle 0.55946 (30937) hydrogen bonds : bond 0.05479 ( 1045) hydrogen bonds : angle 4.55717 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 459 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6803 (ptm) cc_final: 0.6389 (ptm) REVERT: A 199 ILE cc_start: 0.5103 (OUTLIER) cc_final: 0.4648 (mp) REVERT: A 224 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7980 (ttp80) REVERT: A 340 VAL cc_start: 0.8734 (m) cc_final: 0.8341 (t) REVERT: A 414 PHE cc_start: 0.8295 (p90) cc_final: 0.7869 (p90) REVERT: A 521 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7939 (mmm-85) REVERT: A 599 ARG cc_start: 0.8549 (tpt170) cc_final: 0.8212 (tpt170) REVERT: B 323 VAL cc_start: 0.8535 (t) cc_final: 0.8289 (m) REVERT: B 340 VAL cc_start: 0.8741 (p) cc_final: 0.8488 (t) REVERT: B 515 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8398 (mp) REVERT: B 620 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: C 270 GLU cc_start: 0.7598 (pt0) cc_final: 0.7329 (pt0) REVERT: C 277 GLN cc_start: 0.8189 (mp10) cc_final: 0.7780 (mp10) REVERT: C 414 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7491 (p90) REVERT: C 425 GLU cc_start: 0.8318 (tt0) cc_final: 0.8100 (tt0) REVERT: C 467 GLU cc_start: 0.7987 (tt0) cc_final: 0.7768 (tt0) REVERT: C 498 ARG cc_start: 0.5775 (OUTLIER) cc_final: 0.5408 (tpp-160) REVERT: C 620 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: D 109 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 122 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6580 (p0) REVERT: D 163 TYR cc_start: 0.8100 (m-80) cc_final: 0.7814 (m-80) REVERT: D 230 ASP cc_start: 0.7329 (m-30) cc_final: 0.7073 (m-30) REVERT: D 327 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7600 (t) REVERT: D 345 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7792 (mtp85) REVERT: D 414 PHE cc_start: 0.8480 (p90) cc_final: 0.8191 (p90) REVERT: D 515 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8356 (mp) REVERT: E 168 PHE cc_start: 0.6954 (p90) cc_final: 0.6501 (p90) REVERT: E 239 ILE cc_start: 0.4574 (OUTLIER) cc_final: 0.4317 (tp) REVERT: E 480 GLU cc_start: 0.7605 (mp0) cc_final: 0.7222 (mp0) REVERT: E 544 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7711 (ttm-80) REVERT: E 599 ARG cc_start: 0.8557 (tpt90) cc_final: 0.8247 (tmt170) REVERT: E 620 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7371 (m-80) outliers start: 74 outliers final: 47 residues processed: 494 average time/residue: 0.7037 time to fit residues: 388.7554 Evaluate side-chains 518 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 280 optimal weight: 0.7980 chunk 279 optimal weight: 0.0070 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 240 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN B 405 ASN C 410 ASN C 502 ASN D 545 GLN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134840 restraints weight = 33029.783| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.46 r_work: 0.3575 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22709 Z= 0.107 Angle : 0.526 11.629 30937 Z= 0.273 Chirality : 0.042 0.151 3528 Planarity : 0.004 0.050 4019 Dihedral : 4.291 21.396 3064 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.08 % Allowed : 17.69 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.16), residues: 2830 helix: 2.47 (0.20), residues: 706 sheet: 0.83 (0.17), residues: 949 loop : -0.55 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 420 TYR 0.015 0.001 TYR D 143 PHE 0.041 0.001 PHE A 561 TRP 0.030 0.001 TRP B 121 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00233 (22709) covalent geometry : angle 0.52643 (30937) hydrogen bonds : bond 0.04469 ( 1045) hydrogen bonds : angle 4.34401 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 467 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6763 (ptm) cc_final: 0.6339 (ptm) REVERT: A 199 ILE cc_start: 0.5095 (OUTLIER) cc_final: 0.4647 (mp) REVERT: A 224 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (ttp80) REVERT: A 414 PHE cc_start: 0.8263 (p90) cc_final: 0.7830 (p90) REVERT: A 460 MET cc_start: 0.8333 (mtp) cc_final: 0.8124 (mtm) REVERT: A 521 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7891 (mmm-85) REVERT: B 323 VAL cc_start: 0.8523 (t) cc_final: 0.8291 (m) REVERT: B 515 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 620 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: C 270 GLU cc_start: 0.7530 (pt0) cc_final: 0.7273 (pt0) REVERT: C 277 GLN cc_start: 0.8128 (mp10) cc_final: 0.7722 (mp10) REVERT: C 414 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7496 (p90) REVERT: C 425 GLU cc_start: 0.8337 (tt0) cc_final: 0.8126 (tt0) REVERT: C 467 GLU cc_start: 0.7970 (tt0) cc_final: 0.7750 (tt0) REVERT: C 498 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5341 (tpp-160) REVERT: C 620 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: D 109 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 122 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6756 (p0) REVERT: D 163 TYR cc_start: 0.8090 (m-80) cc_final: 0.7800 (m-80) REVERT: D 230 ASP cc_start: 0.7312 (m-30) cc_final: 0.7063 (m-30) REVERT: D 327 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7564 (t) REVERT: D 345 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7794 (mtp85) REVERT: D 414 PHE cc_start: 0.8455 (p90) cc_final: 0.8199 (p90) REVERT: D 500 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7817 (p) REVERT: D 515 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8327 (mp) REVERT: E 168 PHE cc_start: 0.6907 (p90) cc_final: 0.6462 (p90) REVERT: E 239 ILE cc_start: 0.4514 (OUTLIER) cc_final: 0.4266 (tp) REVERT: E 480 GLU cc_start: 0.7593 (mp0) cc_final: 0.7203 (mp0) REVERT: E 599 ARG cc_start: 0.8434 (tpt90) cc_final: 0.7994 (tpt90) REVERT: E 634 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7632 (ttm110) outliers start: 50 outliers final: 30 residues processed: 491 average time/residue: 0.6774 time to fit residues: 373.4813 Evaluate side-chains 500 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 458 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 564 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 83 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 0.0570 chunk 175 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN B 597 GLN C 410 ASN C 502 ASN D 560 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134717 restraints weight = 32937.445| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.45 r_work: 0.3569 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22709 Z= 0.115 Angle : 0.534 11.518 30937 Z= 0.276 Chirality : 0.042 0.155 3528 Planarity : 0.004 0.053 4019 Dihedral : 4.257 21.090 3064 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.16 % Allowed : 18.06 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 2830 helix: 2.50 (0.20), residues: 706 sheet: 0.89 (0.16), residues: 965 loop : -0.51 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 420 TYR 0.018 0.001 TYR A 44 PHE 0.041 0.001 PHE A 561 TRP 0.030 0.001 TRP B 121 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00257 (22709) covalent geometry : angle 0.53438 (30937) hydrogen bonds : bond 0.04693 ( 1045) hydrogen bonds : angle 4.33077 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10893.94 seconds wall clock time: 185 minutes 13.85 seconds (11113.85 seconds total)