Starting phenix.real_space_refine on Mon Aug 25 21:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.map" model { file = "/net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rs9_19473/08_2025/8rs9_19473.cif" } resolution = 3.4 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= 0.007 sd= 0.053 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 137 5.16 5 C 19488 2.51 5 N 5669 2.21 5 O 6065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31359 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5248 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 18, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 317 Chain: "B" Number of atoms: 5242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5242 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 597 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 18, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 321 Chain: "C" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5244 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 18, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 321 Chain: "D" Number of atoms: 5131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5131 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 712 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'ASN:plan1': 11, 'ARG:plan': 22, 'ASP:plan': 20, 'GLU:plan': 21, 'GLN:plan1': 4, 'PHE:plan': 8, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 396 Chain: "E" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5246 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 18, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 317 Chain: "F" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5248 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 18, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 317 Time building chain proxies: 8.26, per 1000 atoms: 0.26 Number of scatterers: 31359 At special positions: 0 Unit cell: (171.14, 172.86, 117.82, 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 137 16.00 O 6065 8.00 N 5669 7.00 C 19488 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: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 18 sheets defined 48.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.699A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.574A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.666A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.318A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.968A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 295 removed outlier: 4.310A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.845A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.569A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.031A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 4.005A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.729A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.877A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.565A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.645A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.653A pdb=" N ILE A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.578A pdb=" N ILE A 633 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 684 through 716 removed outlier: 3.830A pdb=" N THR A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.979A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.552A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.699A pdb=" N PHE B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.171A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 removed outlier: 4.184A pdb=" N ASP B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 206' Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.517A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix removed outlier: 3.631A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.338A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.965A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 removed outlier: 4.317A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.828A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.574A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.038A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.976A pdb=" N LYS B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.711A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.918A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 removed outlier: 3.599A pdb=" N ARG B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.659A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.651A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.593A pdb=" N ILE B 633 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 684 through 716 removed outlier: 3.838A pdb=" N THR B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 removed outlier: 4.008A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 760 removed outlier: 3.576A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 91' Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.801A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix removed outlier: 3.672A pdb=" N HIS C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.328A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.955A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.363A pdb=" N GLU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.831A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 409 through 427 Processing helix chain 'C' and resid 436 through 445 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.648A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.041A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 4.019A pdb=" N LYS C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.751A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.893A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 removed outlier: 3.592A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.642A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.766A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.539A pdb=" N ILE C 633 " --> pdb=" O ASP C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 662 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 684 through 716 removed outlier: 3.830A pdb=" N THR C 688 " --> pdb=" O GLY C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 4.002A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 760 removed outlier: 3.538A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 91' Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.674A pdb=" N GLU D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.533A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix removed outlier: 3.676A pdb=" N HIS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.313A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.936A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 295 removed outlier: 4.341A pdb=" N GLU D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.850A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.718A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 349 through 353' Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 409 through 427 Processing helix chain 'D' and resid 436 through 445 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.592A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.046A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.514A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 removed outlier: 3.682A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.648A pdb=" N PHE D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 removed outlier: 3.575A pdb=" N ARG D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.646A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.513A pdb=" N LYS D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.666A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 removed outlier: 3.586A pdb=" N ILE D 633 " --> pdb=" O ASP D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 662 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 684 through 716 removed outlier: 3.840A pdb=" N THR D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.977A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 760 removed outlier: 3.522A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.668A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.130A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 91' Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 removed outlier: 3.696A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.508A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix removed outlier: 3.666A pdb=" N HIS E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.330A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.938A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 295 removed outlier: 4.347A pdb=" N GLU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.831A pdb=" N GLN E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 409 through 427 Processing helix chain 'E' and resid 436 through 445 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.600A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 495 through 498 Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.032A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.501A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.709A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 removed outlier: 3.644A pdb=" N PHE E 563 " --> pdb=" O VAL E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 removed outlier: 3.584A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.626A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 616 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.646A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 removed outlier: 3.576A pdb=" N ILE E 633 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 662 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 684 through 716 removed outlier: 3.850A pdb=" N THR E 688 " --> pdb=" O GLY E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.956A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 760 removed outlier: 3.566A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 91' Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE F 139 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.750A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix removed outlier: 3.657A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.327A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.962A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 295 removed outlier: 4.360A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.845A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 409 through 427 Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.582A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.029A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.536A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.674A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 removed outlier: 3.671A pdb=" N PHE F 563 " --> pdb=" O VAL F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 removed outlier: 3.573A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.680A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 616 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.707A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 removed outlier: 3.569A pdb=" N ILE F 633 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 684 through 716 removed outlier: 3.861A pdb=" N THR F 688 " --> pdb=" O GLY F 684 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.967A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.547A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.601A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 542 removed outlier: 8.214A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.558A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 542 removed outlier: 8.205A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.581A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 538 through 542 removed outlier: 8.167A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.554A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 538 through 542 removed outlier: 8.224A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.659A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 538 through 542 removed outlier: 8.219A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.627A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.406A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 538 through 542 removed outlier: 8.173A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 1254 hydrogen bonds defined for protein. 3558 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: 4.54 Time building geometry restraints manager: 3.51 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: 9855 1.33 - 1.45: 3543 1.45 - 1.57: 18144 1.57 - 1.69: 0 1.69 - 1.81: 233 Bond restraints: 31775 Sorted by residual: bond pdb=" C TYR E 203 " pdb=" O TYR E 203 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.15e-02 7.56e+03 3.93e+00 bond pdb=" N ILE E 189 " pdb=" CA ILE E 189 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.29e-02 6.01e+03 3.53e+00 bond pdb=" C TYR F 203 " pdb=" O TYR F 203 " ideal model delta sigma weight residual 1.236 1.215 0.020 1.18e-02 7.18e+03 2.93e+00 bond pdb=" CA GLY C 202 " pdb=" C GLY C 202 " ideal model delta sigma weight residual 1.516 1.501 0.015 8.90e-03 1.26e+04 2.76e+00 bond pdb=" N ILE D 189 " pdb=" CA ILE D 189 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.42e-02 4.96e+03 2.67e+00 ... (remaining 31770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 41724 1.66 - 3.32: 1196 3.32 - 4.98: 216 4.98 - 6.64: 20 6.64 - 8.31: 7 Bond angle restraints: 43163 Sorted by residual: angle pdb=" N ILE D 189 " pdb=" CA ILE D 189 " pdb=" C ILE D 189 " ideal model delta sigma weight residual 107.28 115.10 -7.82 1.59e+00 3.96e-01 2.42e+01 angle pdb=" N ILE E 189 " pdb=" CA ILE E 189 " pdb=" C ILE E 189 " ideal model delta sigma weight residual 107.75 114.80 -7.05 1.46e+00 4.69e-01 2.33e+01 angle pdb=" CA PRO D 188 " pdb=" C PRO D 188 " pdb=" O PRO D 188 " ideal model delta sigma weight residual 121.03 115.87 5.16 1.14e+00 7.69e-01 2.05e+01 angle pdb=" N ARG D 191 " pdb=" CA ARG D 191 " pdb=" C ARG D 191 " ideal model delta sigma weight residual 111.28 116.19 -4.91 1.09e+00 8.42e-01 2.03e+01 angle pdb=" CA PRO E 188 " pdb=" C PRO E 188 " pdb=" O PRO E 188 " ideal model delta sigma weight residual 120.97 115.83 5.14 1.17e+00 7.31e-01 1.93e+01 ... (remaining 43158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 17320 17.58 - 35.16: 1689 35.16 - 52.74: 421 52.74 - 70.32: 87 70.32 - 87.90: 31 Dihedral angle restraints: 19548 sinusoidal: 6720 harmonic: 12828 Sorted by residual: dihedral pdb=" CA ARG E 144 " pdb=" C ARG E 144 " pdb=" N PRO E 145 " pdb=" CA PRO E 145 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ARG B 144 " pdb=" C ARG B 144 " pdb=" N PRO B 145 " pdb=" CA PRO B 145 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ARG F 144 " pdb=" C ARG F 144 " pdb=" N PRO F 145 " pdb=" CA PRO F 145 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 19545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3642 0.041 - 0.083: 942 0.083 - 0.124: 420 0.124 - 0.166: 47 0.166 - 0.207: 3 Chirality restraints: 5054 Sorted by residual: chirality pdb=" CA LYS C 190 " pdb=" N LYS C 190 " pdb=" C LYS C 190 " pdb=" CB LYS C 190 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS F 190 " pdb=" N LYS F 190 " pdb=" C LYS F 190 " pdb=" CB LYS F 190 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA TYR F 203 " pdb=" N TYR F 203 " pdb=" C TYR F 203 " pdb=" CB TYR F 203 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 5051 not shown) Planarity restraints: 5846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 371 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO C 372 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 372 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 372 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 187 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C GLU D 187 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU D 187 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO D 188 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 753 " -0.159 9.50e-02 1.11e+02 7.17e-02 3.63e+00 pdb=" NE ARG B 753 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 753 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 753 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 753 " -0.002 2.00e-02 2.50e+03 ... (remaining 5843 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 334 2.59 - 3.17: 29211 3.17 - 3.75: 45260 3.75 - 4.32: 58159 4.32 - 4.90: 94165 Nonbonded interactions: 227129 Sorted by model distance: nonbonded pdb=" NZ LYS E 386 " pdb=" OD1 ASN E 387 " model vdw 2.014 3.120 nonbonded pdb=" NH2 ARG A 465 " pdb=" OE2 GLU B 607 " model vdw 2.051 3.120 nonbonded pdb=" OD1 ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASP E 307 " pdb=" OG SER E 352 " model vdw 2.070 3.040 nonbonded pdb=" O GLU B 546 " pdb=" OG1 THR B 549 " model vdw 2.087 3.040 ... (remaining 227124 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 21 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 553 or (resid 554 through 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 588 \ or (resid 589 through 590 and (name N or name CA or name C or name O or name CB \ )) or resid 591 or (resid 592 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 593 through 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 through 763)) selection = (chain 'B' and (resid 21 through 553 or (resid 554 through 586 and (name N or na \ me CA or name C or name O or name CB )) or resid 587 through 588 or (resid 589 t \ hrough 590 and (name N or name CA or name C or name O or name CB )) or resid 591 \ or (resid 592 and (name N or name CA or name C or name O or name CB )) or (resi \ d 593 through 600 and (name N or name CA or name C or name O or name CB )) or re \ sid 601 through 763)) selection = (chain 'C' and (resid 21 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 553 or (resid 554 through 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 588 \ or (resid 589 through 590 and (name N or name CA or name C or name O or name CB \ )) or resid 591 or (resid 592 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 593 through 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 through 763)) selection = (chain 'D' and (resid 21 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 763)) selection = (chain 'E' and (resid 21 through 553 or (resid 554 through 586 and (name N or na \ me CA or name C or name O or name CB )) or resid 587 through 588 or (resid 589 t \ hrough 590 and (name N or name CA or name C or name O or name CB )) or resid 591 \ or (resid 592 and (name N or name CA or name C or name O or name CB )) or (resi \ d 593 through 600 and (name N or name CA or name C or name O or name CB )) or re \ sid 601 through 763)) selection = (chain 'F' and (resid 21 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 553 or (resid 554 through 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 588 \ or (resid 589 through 590 and (name N or name CA or name C or name O or name CB \ )) or resid 591 or (resid 592 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 593 through 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 through 763)) } 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: 2.170 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: 0.050 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 27.470 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 0.040 31775 Z= 0.161 Angle : 0.665 8.305 43163 Z= 0.385 Chirality : 0.045 0.207 5054 Planarity : 0.004 0.072 5846 Dihedral : 15.769 87.903 11208 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.15 % Allowed : 24.81 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.80 (0.13), residues: 4446 helix: 0.39 (0.13), residues: 1764 sheet: -0.62 (0.31), residues: 372 loop : -2.71 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 753 TYR 0.009 0.001 TYR B 203 PHE 0.025 0.001 PHE F 265 TRP 0.014 0.001 TRP A 454 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00307 (31775) covalent geometry : angle 0.66518 (43163) hydrogen bonds : bond 0.18643 ( 1254) hydrogen bonds : angle 7.34443 ( 3558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 650 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 LYS cc_start: 0.7610 (mmmm) cc_final: 0.6753 (pttt) REVERT: A 709 ARG cc_start: 0.8352 (mpt-90) cc_final: 0.7285 (ptm-80) REVERT: B 512 LYS cc_start: 0.7571 (mmmm) cc_final: 0.6657 (pttt) REVERT: B 709 ARG cc_start: 0.8067 (mpt-90) cc_final: 0.7086 (ptm-80) REVERT: C 512 LYS cc_start: 0.7585 (mmmm) cc_final: 0.6658 (pttt) REVERT: D 512 LYS cc_start: 0.7673 (mmmm) cc_final: 0.6709 (pttt) REVERT: D 709 ARG cc_start: 0.8294 (mpt-90) cc_final: 0.7117 (ptm-80) REVERT: D 720 MET cc_start: -0.2062 (mmm) cc_final: -0.2271 (mmm) REVERT: E 709 ARG cc_start: 0.8049 (mpt-90) cc_final: 0.7043 (ptm-80) REVERT: F 464 LEU cc_start: 0.8280 (mp) cc_final: 0.7882 (mp) REVERT: F 512 LYS cc_start: 0.7603 (mmmm) cc_final: 0.6726 (pttt) REVERT: F 709 ARG cc_start: 0.8299 (mpt-90) cc_final: 0.7182 (ptm-80) outliers start: 4 outliers final: 3 residues processed: 653 average time/residue: 0.2112 time to fit residues: 206.4364 Evaluate side-chains 294 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain E residue 476 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 460 ASN A 533 ASN A 558 ASN A 660 ASN B 460 ASN B 494 GLN C 260 ASN C 460 ASN C 494 GLN C 660 ASN D 616 ASN D 660 ASN D 680 ASN E 260 ASN E 404 HIS E 460 ASN E 641 GLN F 382 GLN F 558 ASN F 568 GLN F 660 ASN F 680 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.175484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.127296 restraints weight = 63901.331| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.08 r_work: 0.3752 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31775 Z= 0.159 Angle : 0.665 9.957 43163 Z= 0.346 Chirality : 0.047 0.148 5054 Planarity : 0.005 0.055 5846 Dihedral : 4.900 56.902 4718 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.01 % Allowed : 21.45 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.42 (0.13), residues: 4446 helix: 0.77 (0.12), residues: 1770 sheet: -0.88 (0.28), residues: 432 loop : -2.49 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 599 TYR 0.012 0.001 TYR B 203 PHE 0.016 0.002 PHE F 363 TRP 0.020 0.003 TRP C 454 HIS 0.012 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00363 (31775) covalent geometry : angle 0.66549 (43163) hydrogen bonds : bond 0.04870 ( 1254) hydrogen bonds : angle 5.26615 ( 3558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 310 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8936 (ttm170) cc_final: 0.8628 (tpm170) REVERT: A 421 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 512 LYS cc_start: 0.7983 (mmmm) cc_final: 0.6955 (pttt) REVERT: A 709 ARG cc_start: 0.8292 (mpt-90) cc_final: 0.7242 (ptm-80) REVERT: B 349 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8744 (tpm170) REVERT: B 709 ARG cc_start: 0.8084 (mpt-90) cc_final: 0.7049 (ptm-80) REVERT: C 349 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8694 (tpm170) REVERT: C 465 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7443 (mmt180) REVERT: D 709 ARG cc_start: 0.8186 (mpt-90) cc_final: 0.7114 (ptm-80) REVERT: E 397 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: E 709 ARG cc_start: 0.8016 (mpt-90) cc_final: 0.7010 (ptm-80) REVERT: E 744 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7674 (mtp85) REVERT: F 349 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8646 (tpm170) REVERT: F 704 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7033 (pp20) outliers start: 110 outliers final: 48 residues processed: 404 average time/residue: 0.1874 time to fit residues: 121.1166 Evaluate side-chains 308 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 525 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 673 GLU Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 404 optimal weight: 9.9990 chunk 15 optimal weight: 0.0060 chunk 73 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 302 optimal weight: 0.0570 chunk 389 optimal weight: 5.9990 chunk 365 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 overall best weight: 3.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 660 ASN A 680 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 660 ASN C 680 ASN D 404 HIS D 660 ASN D 714 GLN ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN F 260 ASN F 404 HIS F 660 ASN F 714 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.171084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.124948 restraints weight = 65188.935| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.11 r_work: 0.3702 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31775 Z= 0.156 Angle : 0.609 8.831 43163 Z= 0.318 Chirality : 0.046 0.139 5054 Planarity : 0.005 0.055 5846 Dihedral : 4.652 58.239 4716 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.60 % Allowed : 21.85 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.21 (0.13), residues: 4446 helix: 0.79 (0.12), residues: 1812 sheet: -0.96 (0.26), residues: 492 loop : -2.26 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 313 TYR 0.019 0.002 TYR B 203 PHE 0.025 0.002 PHE F 265 TRP 0.011 0.002 TRP C 476 HIS 0.006 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00361 (31775) covalent geometry : angle 0.60934 (43163) hydrogen bonds : bond 0.04421 ( 1254) hydrogen bonds : angle 4.89331 ( 3558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 279 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 349 ARG cc_start: 0.8910 (ttm170) cc_final: 0.8695 (tpm170) REVERT: A 421 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 709 ARG cc_start: 0.8301 (mpt-90) cc_final: 0.7220 (ptm-80) REVERT: B 349 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (tpm170) REVERT: B 531 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 567 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7354 (mpp80) REVERT: B 709 ARG cc_start: 0.8083 (mpt-90) cc_final: 0.6963 (ttp80) REVERT: B 737 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6870 (mt-10) REVERT: C 465 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7513 (mmt180) REVERT: C 550 MET cc_start: 0.7740 (mtt) cc_final: 0.7234 (mtm) REVERT: D 267 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: D 709 ARG cc_start: 0.8235 (mpt-90) cc_final: 0.7118 (ptm-80) REVERT: D 720 MET cc_start: -0.2549 (tpp) cc_final: -0.2886 (mmm) REVERT: E 397 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: E 421 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: E 477 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: E 709 ARG cc_start: 0.8043 (mpt-90) cc_final: 0.7033 (ptm-80) REVERT: E 730 GLU cc_start: 0.7251 (pt0) cc_final: 0.6910 (pm20) REVERT: F 349 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8627 (tpm170) outliers start: 126 outliers final: 59 residues processed: 391 average time/residue: 0.1823 time to fit residues: 113.4168 Evaluate side-chains 317 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 525 THR Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 169 optimal weight: 9.9990 chunk 129 optimal weight: 0.0770 chunk 342 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 chunk 74 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 239 optimal weight: 0.0870 chunk 150 optimal weight: 40.0000 chunk 203 optimal weight: 0.9990 chunk 401 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 660 ASN C 443 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 660 ASN E 494 GLN F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.171556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125572 restraints weight = 63646.768| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 4.23 r_work: 0.3719 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31775 Z= 0.123 Angle : 0.578 8.455 43163 Z= 0.295 Chirality : 0.045 0.187 5054 Planarity : 0.004 0.053 5846 Dihedral : 4.456 58.175 4716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.05 % Allowed : 22.29 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.04 (0.13), residues: 4446 helix: 1.00 (0.12), residues: 1818 sheet: -1.07 (0.26), residues: 516 loop : -2.20 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.019 0.001 TYR C 203 PHE 0.025 0.001 PHE D 674 TRP 0.012 0.001 TRP E 454 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00286 (31775) covalent geometry : angle 0.57838 (43163) hydrogen bonds : bond 0.03907 ( 1254) hydrogen bonds : angle 4.62301 ( 3558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 288 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: A 349 ARG cc_start: 0.8956 (ttm170) cc_final: 0.8695 (tpm170) REVERT: A 421 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 678 MET cc_start: 0.8561 (mmm) cc_final: 0.8313 (tpp) REVERT: B 567 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7356 (mpp80) REVERT: B 678 MET cc_start: 0.8157 (tpp) cc_final: 0.7906 (tpp) REVERT: B 737 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: C 267 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: C 397 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: C 465 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7500 (mmm160) REVERT: C 550 MET cc_start: 0.7653 (mtt) cc_final: 0.7255 (mtm) REVERT: D 267 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: D 275 MET cc_start: 0.8454 (mmp) cc_final: 0.8244 (mmm) REVERT: D 737 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: E 397 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: E 421 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: E 567 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7396 (mpp80) REVERT: E 709 ARG cc_start: 0.7944 (mpt-90) cc_final: 0.6856 (ttp80) REVERT: F 349 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8621 (tpm170) REVERT: F 427 MET cc_start: 0.8551 (tpp) cc_final: 0.8189 (tpp) REVERT: F 644 TYR cc_start: 0.8060 (t80) cc_final: 0.7697 (t80) outliers start: 111 outliers final: 59 residues processed: 389 average time/residue: 0.1878 time to fit residues: 118.0984 Evaluate side-chains 332 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 137 optimal weight: 10.0000 chunk 349 optimal weight: 0.0470 chunk 295 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 416 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 16 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 231 optimal weight: 50.0000 chunk 59 optimal weight: 7.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 404 HIS C 533 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.171369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.125290 restraints weight = 63866.614| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 4.21 r_work: 0.3712 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31775 Z= 0.114 Angle : 0.562 8.354 43163 Z= 0.286 Chirality : 0.045 0.157 5054 Planarity : 0.004 0.053 5846 Dihedral : 4.292 58.320 4716 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.98 % Allowed : 22.98 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.13), residues: 4446 helix: 1.08 (0.13), residues: 1836 sheet: -1.05 (0.26), residues: 516 loop : -2.15 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 313 TYR 0.018 0.001 TYR C 203 PHE 0.027 0.001 PHE F 265 TRP 0.019 0.002 TRP B 454 HIS 0.003 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00263 (31775) covalent geometry : angle 0.56219 (43163) hydrogen bonds : bond 0.03692 ( 1254) hydrogen bonds : angle 4.44794 ( 3558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 296 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: A 349 ARG cc_start: 0.8946 (ttm170) cc_final: 0.8644 (tpm170) REVERT: A 393 ASP cc_start: 0.7704 (p0) cc_final: 0.7472 (t0) REVERT: A 421 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 678 MET cc_start: 0.8502 (mmm) cc_final: 0.8230 (tpp) REVERT: A 709 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.7167 (ptm-80) REVERT: B 567 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7368 (mpp80) REVERT: B 737 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: C 267 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: C 294 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: C 465 ARG cc_start: 0.8278 (mmt90) cc_final: 0.7591 (mmt180) REVERT: C 550 MET cc_start: 0.7564 (mtt) cc_final: 0.7260 (mtm) REVERT: D 267 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: D 458 GLN cc_start: 0.7988 (mp10) cc_final: 0.7612 (mp10) REVERT: D 678 MET cc_start: 0.8331 (mmm) cc_final: 0.7967 (mmm) REVERT: D 720 MET cc_start: -0.2294 (tpp) cc_final: -0.2511 (mmm) REVERT: D 737 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: E 397 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: E 421 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: E 534 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: E 567 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7441 (mpp80) REVERT: F 349 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8582 (tpm170) REVERT: F 427 MET cc_start: 0.8600 (tpp) cc_final: 0.8241 (tpt) REVERT: F 465 ARG cc_start: 0.6993 (mmt90) cc_final: 0.6502 (mmm160) REVERT: F 508 MET cc_start: 0.7204 (tpt) cc_final: 0.6864 (tpt) outliers start: 109 outliers final: 55 residues processed: 388 average time/residue: 0.2051 time to fit residues: 127.0962 Evaluate side-chains 331 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 195 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 413 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 409 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 276 optimal weight: 30.0000 chunk 317 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 494 GLN B 260 ASN B 660 ASN C 602 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 398 GLN E 533 ASN F 404 HIS F 490 GLN F 533 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.172134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125827 restraints weight = 63416.907| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 4.35 r_work: 0.3745 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31775 Z= 0.103 Angle : 0.554 9.326 43163 Z= 0.279 Chirality : 0.044 0.131 5054 Planarity : 0.004 0.052 5846 Dihedral : 4.181 58.275 4716 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.39 % Allowed : 23.57 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.80 (0.13), residues: 4446 helix: 1.19 (0.13), residues: 1842 sheet: -0.94 (0.26), residues: 516 loop : -2.09 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.017 0.001 TYR C 203 PHE 0.025 0.001 PHE F 265 TRP 0.018 0.002 TRP E 454 HIS 0.003 0.001 HIS F 735 Details of bonding type rmsd covalent geometry : bond 0.00235 (31775) covalent geometry : angle 0.55381 (43163) hydrogen bonds : bond 0.03481 ( 1254) hydrogen bonds : angle 4.36676 ( 3558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 280 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: A 349 ARG cc_start: 0.9048 (ttm170) cc_final: 0.8537 (tpm170) REVERT: A 393 ASP cc_start: 0.7547 (p0) cc_final: 0.7334 (t0) REVERT: A 421 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 678 MET cc_start: 0.8394 (mmm) cc_final: 0.7347 (mmp) REVERT: B 427 MET cc_start: 0.8577 (tpp) cc_final: 0.8305 (tpp) REVERT: B 567 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7379 (mpp80) REVERT: B 737 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: C 267 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: C 397 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: C 427 MET cc_start: 0.8458 (tpp) cc_final: 0.8206 (tpp) REVERT: C 465 ARG cc_start: 0.8210 (mmt90) cc_final: 0.7531 (mmt180) REVERT: C 550 MET cc_start: 0.7498 (mtt) cc_final: 0.7236 (mtm) REVERT: D 267 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: D 458 GLN cc_start: 0.7949 (mp10) cc_final: 0.7633 (mp10) REVERT: D 550 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6433 (mtp) REVERT: D 737 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: E 397 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: E 421 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: E 534 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: E 567 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7473 (mpp80) REVERT: F 349 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8571 (tpm170) REVERT: F 397 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: F 465 ARG cc_start: 0.7029 (mmt90) cc_final: 0.6575 (mmm160) REVERT: F 678 MET cc_start: 0.8147 (tpp) cc_final: 0.7415 (mmp) outliers start: 93 outliers final: 65 residues processed: 363 average time/residue: 0.2016 time to fit residues: 118.1118 Evaluate side-chains 336 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 256 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 210 optimal weight: 9.9990 chunk 325 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 377 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 291 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 41 optimal weight: 0.0170 chunk 432 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 296 optimal weight: 50.0000 overall best weight: 1.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 398 GLN E 660 ASN F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.171454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.124816 restraints weight = 63772.358| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.26 r_work: 0.3713 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31775 Z= 0.111 Angle : 0.553 10.680 43163 Z= 0.278 Chirality : 0.044 0.150 5054 Planarity : 0.004 0.052 5846 Dihedral : 4.089 58.286 4716 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.05 % Allowed : 23.28 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.70 (0.13), residues: 4446 helix: 1.28 (0.13), residues: 1812 sheet: -0.21 (0.27), residues: 432 loop : -2.14 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 700 TYR 0.017 0.001 TYR C 203 PHE 0.025 0.001 PHE C 674 TRP 0.013 0.002 TRP E 454 HIS 0.003 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00258 (31775) covalent geometry : angle 0.55346 (43163) hydrogen bonds : bond 0.03476 ( 1254) hydrogen bonds : angle 4.31741 ( 3558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 273 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 349 ARG cc_start: 0.8985 (ttm170) cc_final: 0.8558 (tpm170) REVERT: A 421 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 678 MET cc_start: 0.8391 (mmm) cc_final: 0.7925 (mmm) REVERT: B 427 MET cc_start: 0.8537 (tpp) cc_final: 0.8145 (tpp) REVERT: B 567 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7392 (mpp80) REVERT: B 737 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: C 267 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 294 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: C 388 MET cc_start: 0.6934 (mmp) cc_final: 0.6594 (mmm) REVERT: C 397 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: C 465 ARG cc_start: 0.8278 (mmt90) cc_final: 0.7701 (mmt180) REVERT: C 678 MET cc_start: 0.7838 (mmm) cc_final: 0.7558 (mmm) REVERT: D 267 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: D 458 GLN cc_start: 0.7975 (mp10) cc_final: 0.7616 (mp10) REVERT: D 678 MET cc_start: 0.8295 (mmm) cc_final: 0.7616 (mmm) REVERT: D 720 MET cc_start: -0.2480 (tpp) cc_final: -0.2680 (mmm) REVERT: D 737 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: E 397 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: E 421 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: E 427 MET cc_start: 0.8640 (tpp) cc_final: 0.8277 (tpp) REVERT: E 534 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: E 567 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7465 (mpp80) REVERT: F 349 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8544 (tpm170) REVERT: F 397 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: F 465 ARG cc_start: 0.6998 (mmt90) cc_final: 0.6569 (mmm160) REVERT: F 678 MET cc_start: 0.8229 (tpp) cc_final: 0.7426 (mmp) REVERT: F 757 MET cc_start: 0.8813 (mmm) cc_final: 0.8475 (tpp) outliers start: 111 outliers final: 71 residues processed: 367 average time/residue: 0.1837 time to fit residues: 109.7473 Evaluate side-chains 347 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 261 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 193 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 380 optimal weight: 0.0570 chunk 0 optimal weight: 50.0000 chunk 412 optimal weight: 20.0000 chunk 366 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 424 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 602 ASN B 404 HIS B 660 ASN C 602 ASN D 494 GLN D 660 ASN E 398 GLN E 602 ASN E 660 ASN F 404 HIS ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.172138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126574 restraints weight = 63444.861| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.32 r_work: 0.3732 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31775 Z= 0.097 Angle : 0.547 10.555 43163 Z= 0.273 Chirality : 0.044 0.142 5054 Planarity : 0.004 0.051 5846 Dihedral : 4.035 58.303 4716 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.17 % Allowed : 24.12 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.57 (0.13), residues: 4446 helix: 1.39 (0.13), residues: 1812 sheet: -0.12 (0.28), residues: 432 loop : -2.07 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 322 TYR 0.017 0.001 TYR C 203 PHE 0.023 0.001 PHE F 265 TRP 0.016 0.002 TRP A 476 HIS 0.003 0.001 HIS F 735 Details of bonding type rmsd covalent geometry : bond 0.00217 (31775) covalent geometry : angle 0.54716 (43163) hydrogen bonds : bond 0.03242 ( 1254) hydrogen bonds : angle 4.21826 ( 3558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 284 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 349 ARG cc_start: 0.8896 (ttm170) cc_final: 0.8515 (tpm170) REVERT: A 393 ASP cc_start: 0.7674 (p0) cc_final: 0.7369 (t0) REVERT: A 421 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: A 678 MET cc_start: 0.8317 (mmm) cc_final: 0.7339 (mmp) REVERT: B 267 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: B 567 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7472 (mpp80) REVERT: B 674 PHE cc_start: 0.5573 (t80) cc_final: 0.5300 (t80) REVERT: B 678 MET cc_start: 0.7777 (mmm) cc_final: 0.6915 (mmp) REVERT: B 737 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: C 267 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: C 294 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 397 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: C 427 MET cc_start: 0.8487 (tpp) cc_final: 0.8185 (tpt) REVERT: C 465 ARG cc_start: 0.8311 (mmt90) cc_final: 0.7736 (mmt180) REVERT: C 678 MET cc_start: 0.7646 (mmm) cc_final: 0.7424 (mmm) REVERT: D 267 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: D 458 GLN cc_start: 0.7945 (mp10) cc_final: 0.7583 (mp10) REVERT: D 678 MET cc_start: 0.8217 (mmm) cc_final: 0.7185 (mmp) REVERT: D 737 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: D 757 MET cc_start: 0.8824 (mmm) cc_final: 0.8566 (tpp) REVERT: E 397 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: E 421 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: E 427 MET cc_start: 0.8628 (tpp) cc_final: 0.8399 (tpp) REVERT: E 534 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: E 567 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7498 (mpp80) REVERT: E 678 MET cc_start: 0.7786 (mmm) cc_final: 0.7157 (mmm) REVERT: E 757 MET cc_start: 0.8881 (mmm) cc_final: 0.8633 (tpp) REVERT: F 349 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (tpm170) REVERT: F 397 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: F 427 MET cc_start: 0.8663 (tpp) cc_final: 0.8268 (tpp) REVERT: F 465 ARG cc_start: 0.6993 (mmt90) cc_final: 0.6570 (mmm160) REVERT: F 757 MET cc_start: 0.8859 (mmm) cc_final: 0.8536 (tpp) outliers start: 87 outliers final: 58 residues processed: 359 average time/residue: 0.2014 time to fit residues: 116.0597 Evaluate side-chains 337 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 GLN Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 266 optimal weight: 0.5980 chunk 273 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 370 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN D 660 ASN E 398 GLN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.168243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122414 restraints weight = 63815.168| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.11 r_work: 0.3683 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31775 Z= 0.180 Angle : 0.630 11.813 43163 Z= 0.320 Chirality : 0.047 0.156 5054 Planarity : 0.005 0.055 5846 Dihedral : 4.255 59.681 4716 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.06 % Allowed : 24.33 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.92 (0.13), residues: 4446 helix: 1.05 (0.12), residues: 1800 sheet: -0.50 (0.27), residues: 432 loop : -2.16 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 599 TYR 0.017 0.001 TYR B 203 PHE 0.025 0.002 PHE F 265 TRP 0.015 0.002 TRP A 476 HIS 0.007 0.002 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00426 (31775) covalent geometry : angle 0.63011 (43163) hydrogen bonds : bond 0.04208 ( 1254) hydrogen bonds : angle 4.63978 ( 3558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: A 421 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: B 427 MET cc_start: 0.8649 (tpp) cc_final: 0.8301 (tpp) REVERT: B 564 ASP cc_start: 0.8464 (t70) cc_final: 0.8244 (t0) REVERT: B 567 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7476 (mpp80) REVERT: B 674 PHE cc_start: 0.5775 (t80) cc_final: 0.5560 (t80) REVERT: B 730 GLU cc_start: 0.7168 (pt0) cc_final: 0.6936 (pm20) REVERT: B 737 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6799 (mt-10) REVERT: C 267 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: C 397 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: C 427 MET cc_start: 0.8489 (tpp) cc_final: 0.8199 (tpp) REVERT: C 535 CYS cc_start: 0.8075 (t) cc_final: 0.7724 (t) REVERT: C 678 MET cc_start: 0.7765 (mmm) cc_final: 0.7544 (mmm) REVERT: D 267 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: D 349 ARG cc_start: 0.8573 (tpm170) cc_final: 0.8329 (tpm170) REVERT: D 458 GLN cc_start: 0.8046 (mp10) cc_final: 0.7608 (mp10) REVERT: D 678 MET cc_start: 0.8313 (mmm) cc_final: 0.7718 (mmm) REVERT: D 737 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: E 421 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: E 427 MET cc_start: 0.8574 (tpp) cc_final: 0.8332 (tpp) REVERT: E 567 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7456 (mpp80) REVERT: F 388 MET cc_start: 0.7333 (mmp) cc_final: 0.6938 (mmm) REVERT: F 397 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: F 427 MET cc_start: 0.8629 (tpp) cc_final: 0.8229 (tpp) REVERT: F 465 ARG cc_start: 0.7088 (mmt90) cc_final: 0.6700 (mmm160) outliers start: 84 outliers final: 63 residues processed: 336 average time/residue: 0.1841 time to fit residues: 101.1266 Evaluate side-chains 323 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 26 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 357 optimal weight: 2.9990 chunk 377 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 421 optimal weight: 5.9990 chunk 247 optimal weight: 0.0470 chunk 322 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 311 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 558 ASN D 660 ASN E 602 ASN E 660 ASN ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.171108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.124038 restraints weight = 63130.842| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.72 r_work: 0.3637 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31775 Z= 0.193 Angle : 0.649 12.580 43163 Z= 0.330 Chirality : 0.048 0.145 5054 Planarity : 0.005 0.054 5846 Dihedral : 4.462 55.691 4714 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.92 % Allowed : 24.66 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.15 (0.13), residues: 4446 helix: 0.79 (0.12), residues: 1800 sheet: -0.83 (0.27), residues: 402 loop : -2.14 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 753 TYR 0.017 0.002 TYR C 203 PHE 0.031 0.002 PHE C 674 TRP 0.016 0.002 TRP A 476 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00451 (31775) covalent geometry : angle 0.64876 (43163) hydrogen bonds : bond 0.04382 ( 1254) hydrogen bonds : angle 4.88855 ( 3558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: A 349 ARG cc_start: 0.8879 (ttm170) cc_final: 0.8562 (tpm170) REVERT: A 421 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: A 678 MET cc_start: 0.8430 (mmm) cc_final: 0.8200 (mmm) REVERT: A 730 GLU cc_start: 0.7392 (pt0) cc_final: 0.7128 (pm20) REVERT: B 219 MET cc_start: 0.8777 (mtp) cc_final: 0.8004 (ttm) REVERT: B 427 MET cc_start: 0.8716 (tpp) cc_final: 0.8498 (tpp) REVERT: B 535 CYS cc_start: 0.8218 (t) cc_final: 0.8005 (t) REVERT: B 564 ASP cc_start: 0.8438 (t70) cc_final: 0.8213 (t0) REVERT: B 567 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7686 (mpp80) REVERT: B 674 PHE cc_start: 0.5763 (t80) cc_final: 0.5494 (t80) REVERT: B 678 MET cc_start: 0.7873 (mmm) cc_final: 0.6656 (mmp) REVERT: B 737 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: C 267 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: C 397 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: C 427 MET cc_start: 0.8561 (tpp) cc_final: 0.8329 (tpp) REVERT: C 535 CYS cc_start: 0.8185 (t) cc_final: 0.7928 (t) REVERT: C 678 MET cc_start: 0.7838 (mmm) cc_final: 0.7622 (mmm) REVERT: D 267 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: D 458 GLN cc_start: 0.8166 (mp10) cc_final: 0.7718 (mp10) REVERT: D 678 MET cc_start: 0.8446 (mmm) cc_final: 0.7346 (mmp) REVERT: D 737 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: E 219 MET cc_start: 0.8885 (mtp) cc_final: 0.8123 (ttm) REVERT: E 421 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: E 427 MET cc_start: 0.8623 (tpp) cc_final: 0.8298 (tpp) REVERT: E 567 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7552 (mpp80) REVERT: E 674 PHE cc_start: 0.5827 (t80) cc_final: 0.5417 (t80) REVERT: E 678 MET cc_start: 0.7914 (mmm) cc_final: 0.6954 (mmm) REVERT: F 397 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: F 427 MET cc_start: 0.8636 (tpp) cc_final: 0.8246 (tpp) REVERT: F 465 ARG cc_start: 0.7026 (mmt90) cc_final: 0.6702 (mmm160) REVERT: F 535 CYS cc_start: 0.7993 (t) cc_final: 0.7661 (t) outliers start: 80 outliers final: 65 residues processed: 335 average time/residue: 0.1809 time to fit residues: 98.7289 Evaluate side-chains 320 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 415 CYS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 364 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 0 optimal weight: 60.0000 chunk 177 optimal weight: 10.0000 chunk 11 optimal weight: 50.0000 chunk 174 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 263 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 229 optimal weight: 50.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN D 660 ASN E 660 ASN F 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.169709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122576 restraints weight = 63609.187| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.16 r_work: 0.3642 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31775 Z= 0.146 Angle : 0.604 10.045 43163 Z= 0.305 Chirality : 0.046 0.141 5054 Planarity : 0.004 0.053 5846 Dihedral : 4.285 55.966 4714 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.92 % Allowed : 24.95 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.13), residues: 4446 helix: 0.93 (0.12), residues: 1800 sheet: -0.73 (0.28), residues: 402 loop : -2.11 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.017 0.001 TYR C 203 PHE 0.030 0.001 PHE F 674 TRP 0.012 0.002 TRP E 454 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00342 (31775) covalent geometry : angle 0.60445 (43163) hydrogen bonds : bond 0.04007 ( 1254) hydrogen bonds : angle 4.69872 ( 3558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9360.61 seconds wall clock time: 159 minutes 52.60 seconds (9592.60 seconds total)