Starting phenix.real_space_refine on Wed May 28 17:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rs9_19473/05_2025/8rs9_19473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rs9_19473/05_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_19473/05_2025/8rs9_19473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rs9_19473/05_2025/8rs9_19473.map" model { file = "/net/cci-nas-00/data/ceres_data/8rs9_19473/05_2025/8rs9_19473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rs9_19473/05_2025/8rs9_19473.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 18} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 18} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 18} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 11, 'ASP:plan': 20, 'PHE:plan': 8, 'GLU:plan': 21, 'ARG:plan': 22} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 18} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 317 Time building chain proxies: 18.37, per 1000 atoms: 0.59 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: 8.78 Conformation dependent library (CDL) restraints added in 4.9 seconds 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: 4.39 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: 10.75 Time building geometry restraints manager: 10.05 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 70.230 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (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 TRP 0.014 0.001 TRP A 454 HIS 0.003 0.001 HIS C 384 PHE 0.025 0.001 PHE F 265 TYR 0.009 0.001 TYR B 203 ARG 0.014 0.001 ARG D 753 Details of bonding type rmsd hydrogen bonds : bond 0.18643 ( 1254) hydrogen bonds : angle 7.34443 ( 3558) covalent geometry : bond 0.00307 (31775) covalent geometry : angle 0.66518 (43163) *********************** 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 : 3.687 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: 0.5105 time to fit residues: 500.7808 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 : 3.602 ------------------------------------------------------------------------------- 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 374 optimal weight: 50.0000 chunk 336 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 227 optimal weight: 30.0000 chunk 179 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 558 ASN A 660 ASN B 460 ASN B 494 GLN C 260 ASN C 460 ASN C 494 GLN C 558 ASN C 660 ASN D 616 ASN D 660 ASN D 680 ASN E 260 ASN E 404 HIS E 460 ASN E 533 ASN E 603 GLN E 641 GLN F 382 GLN F 558 ASN F 568 GLN F 603 GLN F 660 ASN F 680 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.171822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.124575 restraints weight = 64810.539| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.17 r_work: 0.3713 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31775 Z= 0.206 Angle : 0.711 9.115 43163 Z= 0.372 Chirality : 0.049 0.165 5054 Planarity : 0.005 0.058 5846 Dihedral : 5.004 57.635 4718 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.60 % Allowed : 21.63 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 4446 helix: 0.47 (0.12), residues: 1776 sheet: -1.06 (0.28), residues: 432 loop : -2.53 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 476 HIS 0.010 0.002 HIS C 226 PHE 0.018 0.002 PHE E 736 TYR 0.013 0.002 TYR B 203 ARG 0.007 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 1254) hydrogen bonds : angle 5.41437 ( 3558) covalent geometry : bond 0.00472 (31775) covalent geometry : angle 0.71110 (43163) *********************** 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 422 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 296 time to evaluate : 3.436 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: 0.9022 (ttm170) cc_final: 0.8740 (tpm170) REVERT: A 421 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: A 709 ARG cc_start: 0.8272 (mpt-90) cc_final: 0.7221 (ptm-80) REVERT: B 349 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (tpm170) REVERT: C 349 ARG cc_start: 0.8993 (ttm170) cc_final: 0.8723 (tpm170) REVERT: D 267 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: D 709 ARG cc_start: 0.8224 (mpt-90) cc_final: 0.7164 (ptm-80) REVERT: E 349 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8819 (tpm170) REVERT: E 397 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: E 709 ARG cc_start: 0.8121 (mpt-90) cc_final: 0.7012 (ptm-80) REVERT: E 730 GLU cc_start: 0.7066 (pt0) cc_final: 0.6840 (pm20) REVERT: E 744 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7629 (mtp85) REVERT: F 349 ARG cc_start: 0.8944 (ttm170) cc_final: 0.8682 (tpm170) REVERT: F 704 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7022 (pp20) REVERT: F 709 ARG cc_start: 0.8193 (mpt-90) cc_final: 0.7178 (ptm-80) outliers start: 126 outliers final: 50 residues processed: 408 average time/residue: 0.4280 time to fit residues: 281.1434 Evaluate side-chains 315 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 3.401 ------------------------------------------------------------------------------- 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 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 664 SER 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 349 ARG 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 535 CYS Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 213 LEU 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 213 LEU Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS 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 349 ARG 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 525 THR 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 704 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 36 optimal weight: 6.9990 chunk 308 optimal weight: 40.0000 chunk 157 optimal weight: 50.0000 chunk 408 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 378 optimal weight: 50.0000 chunk 265 optimal weight: 5.9990 chunk 246 optimal weight: 0.0040 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 680 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 680 ASN C 260 ASN C 680 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 660 ASN E 260 ASN F 260 ASN F 404 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.169638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.123284 restraints weight = 64189.812| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 4.05 r_work: 0.3676 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31775 Z= 0.185 Angle : 0.637 8.889 43163 Z= 0.336 Chirality : 0.047 0.152 5054 Planarity : 0.005 0.059 5846 Dihedral : 4.825 59.421 4718 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.74 % Allowed : 22.77 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 4446 helix: 0.55 (0.12), residues: 1806 sheet: -1.30 (0.25), residues: 516 loop : -2.35 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 476 HIS 0.006 0.001 HIS F 226 PHE 0.022 0.002 PHE C 736 TYR 0.020 0.002 TYR C 203 ARG 0.011 0.001 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 1254) hydrogen bonds : angle 5.11762 ( 3558) covalent geometry : bond 0.00430 (31775) covalent geometry : angle 0.63743 (43163) *********************** 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 411 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 281 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: A 421 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 709 ARG cc_start: 0.8270 (mpt-90) cc_final: 0.7185 (ptm-80) REVERT: B 567 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7368 (mpp80) REVERT: B 737 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: C 349 ARG cc_start: 0.8986 (ttm170) cc_final: 0.8773 (tpm170) REVERT: D 267 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: D 709 ARG cc_start: 0.8222 (mpt-90) cc_final: 0.7137 (ptm-80) REVERT: E 397 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: E 421 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: E 477 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: E 709 ARG cc_start: 0.8063 (mpt-90) cc_final: 0.6964 (ptm-80) REVERT: E 730 GLU cc_start: 0.7279 (pt0) cc_final: 0.6897 (pm20) REVERT: E 744 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7494 (mtp85) REVERT: F 349 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8657 (tpm170) REVERT: F 427 MET cc_start: 0.8452 (tpp) cc_final: 0.8166 (tpp) REVERT: F 704 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6987 (pp20) REVERT: F 709 ARG cc_start: 0.8075 (mpt-90) cc_final: 0.6988 (ttp80) outliers start: 130 outliers final: 65 residues processed: 395 average time/residue: 0.4134 time to fit residues: 260.8067 Evaluate side-chains 330 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 2.980 ------------------------------------------------------------------------------- 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 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 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 471 VAL 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 737 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 213 LEU 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 574 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 728 VAL 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 368 ASP Chi-restraints excluded: chain D residue 464 LEU 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 699 ILE 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 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 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 347 THR 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 704 GLU Chi-restraints excluded: chain F residue 720 MET 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 365 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 225 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 chunk 432 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 159 optimal weight: 50.0000 chunk 59 optimal weight: 0.5980 chunk 398 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 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 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 660 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 443 ASN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 533 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.168528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.121835 restraints weight = 63952.562| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.39 r_work: 0.3661 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31775 Z= 0.184 Angle : 0.640 8.467 43163 Z= 0.330 Chirality : 0.047 0.231 5054 Planarity : 0.005 0.058 5846 Dihedral : 4.764 59.390 4718 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.25 % Allowed : 22.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4446 helix: 0.59 (0.12), residues: 1806 sheet: -1.52 (0.25), residues: 516 loop : -2.31 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 454 HIS 0.007 0.002 HIS D 226 PHE 0.025 0.002 PHE D 674 TYR 0.019 0.002 TYR C 203 ARG 0.008 0.001 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 1254) hydrogen bonds : angle 4.96491 ( 3558) covalent geometry : bond 0.00429 (31775) covalent geometry : angle 0.64016 (43163) *********************** 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 423 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 279 time to evaluate : 3.582 Fit side-chains revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: A 421 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: B 567 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7484 (mpp80) REVERT: B 737 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: C 267 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: C 362 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7680 (mtt90) REVERT: C 397 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: D 267 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: D 737 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: E 281 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: E 397 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8734 (tt0) REVERT: E 421 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: E 567 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7532 (mpp80) REVERT: E 730 GLU cc_start: 0.7268 (pt0) cc_final: 0.7020 (pm20) REVERT: E 744 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7689 (mtp85) outliers start: 144 outliers final: 83 residues processed: 405 average time/residue: 0.4025 time to fit residues: 263.5510 Evaluate side-chains 352 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 255 time to evaluate : 3.346 ------------------------------------------------------------------------------- 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 347 THR 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 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 GLU 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 347 THR 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 522 CYS 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 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 213 LEU Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 362 ARG 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 448 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 479 ILE 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 613 THR Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 728 VAL 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 464 LEU 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 720 MET 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 281 GLU 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 467 THR Chi-restraints excluded: chain E residue 471 VAL 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 664 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 347 THR 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 664 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 143 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 chunk 435 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 159 optimal weight: 40.0000 chunk 438 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 249 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 558 ASN B 660 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN F 602 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.165124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118456 restraints weight = 65417.692| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 4.58 r_work: 0.3597 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 31775 Z= 0.279 Angle : 0.739 11.037 43163 Z= 0.385 Chirality : 0.051 0.191 5054 Planarity : 0.006 0.064 5846 Dihedral : 5.068 57.722 4718 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 5.62 % Allowed : 24.04 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 4446 helix: 0.19 (0.12), residues: 1806 sheet: -2.07 (0.24), residues: 492 loop : -2.37 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 551 HIS 0.012 0.002 HIS C 226 PHE 0.023 0.002 PHE F 674 TYR 0.024 0.002 TYR F 203 ARG 0.006 0.001 ARG F 239 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1254) hydrogen bonds : angle 5.43434 ( 3558) covalent geometry : bond 0.00652 (31775) covalent geometry : angle 0.73890 (43163) *********************** 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 403 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 249 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: A 421 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 599 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.5600 (mtp85) REVERT: A 674 PHE cc_start: 0.6204 (t80) cc_final: 0.5892 (t80) REVERT: A 678 MET cc_start: 0.8433 (tpp) cc_final: 0.7629 (mmp) REVERT: A 730 GLU cc_start: 0.7412 (pt0) cc_final: 0.6987 (pm20) REVERT: B 567 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7710 (mpp80) REVERT: B 737 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: C 267 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: C 294 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: C 397 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: C 730 GLU cc_start: 0.7403 (pt0) cc_final: 0.7166 (pm20) REVERT: D 267 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: D 730 GLU cc_start: 0.7490 (pt0) cc_final: 0.7107 (pm20) REVERT: D 737 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: D 742 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6973 (t80) REVERT: E 421 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: E 564 ASP cc_start: 0.8537 (t70) cc_final: 0.8332 (t0) REVERT: E 567 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7619 (mpp80) REVERT: E 730 GLU cc_start: 0.7424 (pt0) cc_final: 0.7084 (pm20) REVERT: E 744 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7767 (mtp85) REVERT: F 368 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8236 (p0) REVERT: F 397 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: F 427 MET cc_start: 0.8659 (tpp) cc_final: 0.8349 (tpp) REVERT: F 458 GLN cc_start: 0.8192 (mp10) cc_final: 0.7672 (mp10) REVERT: F 730 GLU cc_start: 0.7561 (pt0) cc_final: 0.7178 (pm20) outliers start: 154 outliers final: 107 residues processed: 389 average time/residue: 0.3931 time to fit residues: 249.1023 Evaluate side-chains 363 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 240 time to evaluate : 3.192 ------------------------------------------------------------------------------- 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 347 THR 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 599 ARG 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 347 THR 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 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 522 CYS 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 606 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 687 LEU 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 213 LEU Chi-restraints excluded: chain C residue 216 ILE 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 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 464 LEU 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 489 LEU 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 720 MET Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain D residue 742 PHE 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 281 GLU 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 471 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 531 ILE 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 687 LEU Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 368 ASP 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 475 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 525 THR Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 722 VAL 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 125 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 326 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 297 optimal weight: 50.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 404 HIS C 533 ASN D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.171939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.123857 restraints weight = 62961.397| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.06 r_work: 0.3654 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31775 Z= 0.117 Angle : 0.588 9.297 43163 Z= 0.301 Chirality : 0.045 0.170 5054 Planarity : 0.005 0.058 5846 Dihedral : 4.638 56.861 4716 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.12 % Allowed : 25.28 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 4446 helix: 0.74 (0.12), residues: 1812 sheet: -1.76 (0.25), residues: 486 loop : -2.23 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 454 HIS 0.003 0.001 HIS C 226 PHE 0.020 0.001 PHE F 674 TYR 0.018 0.001 TYR C 203 ARG 0.005 0.000 ARG E 744 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1254) hydrogen bonds : angle 4.77250 ( 3558) covalent geometry : bond 0.00262 (31775) covalent geometry : angle 0.58809 (43163) *********************** 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 400 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 287 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 349 ARG cc_start: 0.8945 (ttm170) cc_final: 0.8595 (tpm170) REVERT: A 421 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: A 565 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8701 (ttmm) REVERT: A 599 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.5481 (mtp85) REVERT: A 674 PHE cc_start: 0.6175 (t80) cc_final: 0.5742 (t80) REVERT: A 678 MET cc_start: 0.8340 (tpp) cc_final: 0.7360 (mmp) REVERT: A 730 GLU cc_start: 0.7421 (pt0) cc_final: 0.7033 (pm20) REVERT: B 427 MET cc_start: 0.8624 (tpp) cc_final: 0.8098 (tpp) REVERT: B 567 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7673 (mpp80) REVERT: B 737 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: C 267 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: C 397 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: C 427 MET cc_start: 0.8504 (tpp) cc_final: 0.8285 (tpp) REVERT: D 267 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: D 427 MET cc_start: 0.8449 (tpp) cc_final: 0.8172 (tpt) REVERT: D 465 ARG cc_start: 0.7035 (mmt180) cc_final: 0.6766 (mmm160) REVERT: D 550 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6380 (mtp) REVERT: D 730 GLU cc_start: 0.7461 (pt0) cc_final: 0.7112 (pm20) REVERT: D 737 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6958 (mt-10) REVERT: D 742 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6915 (t80) REVERT: E 281 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: E 421 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: E 567 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7526 (mpp80) REVERT: E 730 GLU cc_start: 0.7338 (pt0) cc_final: 0.7091 (pm20) REVERT: E 744 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7614 (mtp85) REVERT: F 349 ARG cc_start: 0.8917 (ttm170) cc_final: 0.8632 (tpm170) REVERT: F 397 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: F 427 MET cc_start: 0.8590 (tpp) cc_final: 0.8236 (tpp) REVERT: F 465 ARG cc_start: 0.6984 (mmt90) cc_final: 0.6634 (mmm160) REVERT: F 508 MET cc_start: 0.7277 (tpt) cc_final: 0.6917 (tpt) REVERT: F 730 GLU cc_start: 0.7564 (pt0) cc_final: 0.7209 (pm20) outliers start: 113 outliers final: 75 residues processed: 388 average time/residue: 0.4177 time to fit residues: 260.9619 Evaluate side-chains 353 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 261 time to evaluate : 3.424 ------------------------------------------------------------------------------- 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 GLU 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 522 CYS 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 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 213 LEU 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 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 484 ASP 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 601 ILE Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain D residue 742 PHE 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 281 GLU Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 492 LEU 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 613 THR Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 744 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 497 VAL 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 266 optimal weight: 8.9990 chunk 336 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 426 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 301 optimal weight: 30.0000 chunk 374 optimal weight: 50.0000 chunk 175 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 404 HIS B 660 ASN C 404 HIS E 404 HIS F 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.168842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122878 restraints weight = 65773.768| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 4.37 r_work: 0.3672 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4708 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= 0.113 Angle : 0.571 10.189 43163 Z= 0.290 Chirality : 0.045 0.149 5054 Planarity : 0.004 0.056 5846 Dihedral : 4.369 57.212 4716 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.16 % Allowed : 24.99 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4446 helix: 1.00 (0.13), residues: 1848 sheet: -1.51 (0.25), residues: 522 loop : -2.21 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 454 HIS 0.003 0.001 HIS D 226 PHE 0.020 0.001 PHE B 674 TYR 0.018 0.001 TYR C 203 ARG 0.004 0.000 ARG E 744 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 1254) hydrogen bonds : angle 4.56963 ( 3558) covalent geometry : bond 0.00258 (31775) covalent geometry : angle 0.57059 (43163) *********************** 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 405 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 291 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 349 ARG cc_start: 0.9030 (ttm170) cc_final: 0.8607 (tpm170) REVERT: A 421 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 599 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5296 (mtp85) REVERT: A 730 GLU cc_start: 0.7298 (pt0) cc_final: 0.7052 (pm20) REVERT: B 427 MET cc_start: 0.8538 (tpp) cc_final: 0.8222 (tpp) REVERT: B 567 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7585 (mpp80) REVERT: B 737 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: C 267 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: C 397 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: C 678 MET cc_start: 0.7811 (mmm) cc_final: 0.6684 (mmp) REVERT: D 267 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: D 465 ARG cc_start: 0.7065 (mmt180) cc_final: 0.6742 (mmm160) REVERT: D 674 PHE cc_start: 0.5611 (t80) cc_final: 0.5334 (t80) REVERT: D 730 GLU cc_start: 0.7274 (pt0) cc_final: 0.7037 (pm20) REVERT: D 737 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: E 281 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: E 421 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: E 476 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.4741 (t-100) REVERT: E 567 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7466 (mpp80) REVERT: E 674 PHE cc_start: 0.5943 (t80) cc_final: 0.5534 (t80) REVERT: E 730 GLU cc_start: 0.7258 (pt0) cc_final: 0.7021 (pm20) REVERT: E 744 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7457 (mtp85) REVERT: F 349 ARG cc_start: 0.8991 (ttm170) cc_final: 0.8640 (tpm170) REVERT: F 397 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: F 465 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6657 (mmm160) outliers start: 114 outliers final: 77 residues processed: 386 average time/residue: 0.3998 time to fit residues: 250.9589 Evaluate side-chains 368 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 276 time to evaluate : 3.474 ------------------------------------------------------------------------------- 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU 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 599 ARG Chi-restraints excluded: chain A residue 601 ILE 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 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 371 ILE 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 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 205 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 265 PHE 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 497 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 484 ASP 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 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU 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 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 E residue 744 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 497 VAL 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 606 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 13 optimal weight: 50.0000 chunk 191 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 155 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 91 optimal weight: 0.0010 chunk 19 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 404 HIS B 660 ASN C 404 HIS E 404 HIS F 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.172024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.124288 restraints weight = 63359.270| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.27 r_work: 0.3660 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31775 Z= 0.118 Angle : 0.575 9.946 43163 Z= 0.291 Chirality : 0.045 0.154 5054 Planarity : 0.004 0.056 5846 Dihedral : 4.310 57.031 4716 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.05 % Allowed : 25.06 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4446 helix: 1.08 (0.13), residues: 1848 sheet: -1.41 (0.25), residues: 522 loop : -2.18 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 454 HIS 0.004 0.001 HIS A 226 PHE 0.022 0.001 PHE E 674 TYR 0.030 0.001 TYR E 203 ARG 0.004 0.000 ARG E 744 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 1254) hydrogen bonds : angle 4.52148 ( 3558) covalent geometry : bond 0.00275 (31775) covalent geometry : angle 0.57461 (43163) *********************** 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 391 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 280 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: A 349 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8601 (tpm170) REVERT: A 421 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 427 MET cc_start: 0.8389 (tpp) cc_final: 0.8111 (tpp) REVERT: A 599 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5283 (mtp85) REVERT: A 674 PHE cc_start: 0.6177 (t80) cc_final: 0.5772 (t80) REVERT: A 678 MET cc_start: 0.8155 (tpp) cc_final: 0.7309 (mmp) REVERT: A 730 GLU cc_start: 0.7434 (pt0) cc_final: 0.7044 (pm20) REVERT: B 427 MET cc_start: 0.8516 (tpp) cc_final: 0.8286 (tpp) REVERT: B 567 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7599 (mpp80) REVERT: B 737 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: C 267 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: C 388 MET cc_start: 0.7087 (mmp) cc_final: 0.6834 (mmm) REVERT: C 427 MET cc_start: 0.8438 (tpp) cc_final: 0.8160 (tpt) REVERT: C 678 MET cc_start: 0.7786 (mmm) cc_final: 0.6532 (mmp) REVERT: D 267 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: D 465 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6719 (mmm160) REVERT: D 678 MET cc_start: 0.8020 (mmm) cc_final: 0.7769 (mmm) REVERT: D 730 GLU cc_start: 0.7372 (pt0) cc_final: 0.7045 (pm20) REVERT: D 737 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: E 421 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: E 427 MET cc_start: 0.8568 (tpp) cc_final: 0.8243 (tpp) REVERT: E 567 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7524 (mpp80) REVERT: E 674 PHE cc_start: 0.5881 (t80) cc_final: 0.5400 (t80) REVERT: E 677 LYS cc_start: 0.7562 (pptt) cc_final: 0.7359 (mmmt) REVERT: E 678 MET cc_start: 0.7800 (mmm) cc_final: 0.6700 (mmp) REVERT: E 730 GLU cc_start: 0.7310 (pt0) cc_final: 0.7076 (pm20) REVERT: E 744 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7494 (mtp85) REVERT: F 349 ARG cc_start: 0.8921 (ttm170) cc_final: 0.8641 (tpm170) REVERT: F 368 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8255 (p0) REVERT: F 397 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: F 427 MET cc_start: 0.8530 (tpp) cc_final: 0.8123 (tpp) REVERT: F 465 ARG cc_start: 0.7010 (mmt90) cc_final: 0.6630 (mmm160) outliers start: 111 outliers final: 80 residues processed: 376 average time/residue: 0.4117 time to fit residues: 251.4512 Evaluate side-chains 366 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 273 time to evaluate : 3.448 ------------------------------------------------------------------------------- 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU 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 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 606 THR 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 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 469 VAL 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 606 THR Chi-restraints excluded: chain B residue 613 THR 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 205 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 267 PHE 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 497 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 464 LEU 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 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL 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 267 PHE 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 469 VAL 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 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 E residue 744 ARG Chi-restraints excluded: chain F residue 368 ASP 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 497 VAL 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 606 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 156 optimal weight: 50.0000 chunk 139 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 341 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 326 optimal weight: 2.9990 chunk 296 optimal weight: 60.0000 chunk 45 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 660 ASN C 296 ASN C 404 HIS D 404 HIS D 624 ASN E 404 HIS F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.172243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125267 restraints weight = 63025.463| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.15 r_work: 0.3672 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4961 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= 0.113 Angle : 0.561 10.453 43163 Z= 0.285 Chirality : 0.045 0.138 5054 Planarity : 0.004 0.056 5846 Dihedral : 4.187 55.144 4716 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.65 % Allowed : 25.03 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4446 helix: 1.12 (0.13), residues: 1872 sheet: -0.83 (0.28), residues: 402 loop : -2.13 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 454 HIS 0.003 0.001 HIS A 226 PHE 0.021 0.001 PHE B 674 TYR 0.025 0.001 TYR E 203 ARG 0.004 0.000 ARG E 744 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 1254) hydrogen bonds : angle 4.43814 ( 3558) covalent geometry : bond 0.00262 (31775) covalent geometry : angle 0.56147 (43163) *********************** 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 383 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 349 ARG cc_start: 0.8959 (ttm170) cc_final: 0.8576 (tpm170) REVERT: A 421 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 427 MET cc_start: 0.8391 (tpp) cc_final: 0.7998 (tpt) REVERT: A 599 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.5244 (mtp85) REVERT: A 674 PHE cc_start: 0.5972 (t80) cc_final: 0.5552 (t80) REVERT: A 678 MET cc_start: 0.8110 (tpp) cc_final: 0.7276 (mmp) REVERT: A 730 GLU cc_start: 0.7349 (pt0) cc_final: 0.6969 (pm20) REVERT: B 427 MET cc_start: 0.8458 (tpp) cc_final: 0.8244 (tpp) REVERT: B 458 GLN cc_start: 0.8094 (mp10) cc_final: 0.7418 (mp10) REVERT: B 567 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7653 (mpp80) REVERT: B 678 MET cc_start: 0.8134 (tpp) cc_final: 0.7406 (mmp) REVERT: B 737 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: C 267 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: C 393 ASP cc_start: 0.7638 (p0) cc_final: 0.7408 (t0) REVERT: C 427 MET cc_start: 0.8475 (tpp) cc_final: 0.8181 (tpt) REVERT: C 678 MET cc_start: 0.7699 (mmm) cc_final: 0.6500 (mmp) REVERT: D 267 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: D 465 ARG cc_start: 0.7055 (mmt180) cc_final: 0.6733 (mmm160) REVERT: D 730 GLU cc_start: 0.7350 (pt0) cc_final: 0.7015 (pm20) REVERT: D 737 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: E 421 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: E 427 MET cc_start: 0.8566 (tpp) cc_final: 0.8241 (tpp) REVERT: E 567 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7590 (mpp80) REVERT: E 678 MET cc_start: 0.7581 (mmm) cc_final: 0.6974 (mmm) REVERT: E 730 GLU cc_start: 0.7459 (pt0) cc_final: 0.7116 (pm20) REVERT: F 349 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8620 (tpm170) REVERT: F 397 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: F 427 MET cc_start: 0.8559 (tpp) cc_final: 0.8211 (tpp) REVERT: F 465 ARG cc_start: 0.7038 (mmt90) cc_final: 0.6646 (mmm160) REVERT: F 678 MET cc_start: 0.8165 (tpp) cc_final: 0.7507 (mmp) REVERT: F 757 MET cc_start: 0.8921 (mmm) cc_final: 0.8652 (tpp) outliers start: 100 outliers final: 79 residues processed: 370 average time/residue: 0.4188 time to fit residues: 250.7405 Evaluate side-chains 361 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 271 time to evaluate : 3.351 ------------------------------------------------------------------------------- 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 265 PHE 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU 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 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 683 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 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 469 VAL 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 606 THR Chi-restraints excluded: chain B residue 613 THR 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 205 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 267 PHE 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 497 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 464 LEU 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 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain E residue 205 ASP 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 467 THR Chi-restraints excluded: chain E residue 469 VAL 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 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 497 VAL 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 606 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 348 optimal weight: 8.9990 chunk 404 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 361 optimal weight: 1.9990 chunk 441 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 394 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 432 optimal weight: 0.0370 chunk 281 optimal weight: 0.0010 overall best weight: 2.0070 ------------------------------------------------------------------------------- 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 404 HIS B 660 ASN C 404 HIS D 260 ASN F 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.172302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125280 restraints weight = 63486.958| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 4.12 r_work: 0.3671 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31775 Z= 0.113 Angle : 0.568 10.462 43163 Z= 0.287 Chirality : 0.045 0.134 5054 Planarity : 0.004 0.055 5846 Dihedral : 4.120 53.498 4716 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.32 % Allowed : 25.32 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4446 helix: 1.23 (0.13), residues: 1836 sheet: -0.63 (0.27), residues: 432 loop : -2.12 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 454 HIS 0.003 0.001 HIS D 226 PHE 0.022 0.001 PHE B 674 TYR 0.024 0.001 TYR E 203 ARG 0.004 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 1254) hydrogen bonds : angle 4.42100 ( 3558) covalent geometry : bond 0.00261 (31775) covalent geometry : angle 0.56785 (43163) ********************** 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 373 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 282 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 349 ARG cc_start: 0.8990 (ttm170) cc_final: 0.8577 (tpm170) REVERT: A 421 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: A 599 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5247 (mtp85) REVERT: A 674 PHE cc_start: 0.5795 (t80) cc_final: 0.5386 (t80) REVERT: A 678 MET cc_start: 0.8098 (tpp) cc_final: 0.7264 (mmp) REVERT: A 730 GLU cc_start: 0.7333 (pt0) cc_final: 0.6975 (pm20) REVERT: B 458 GLN cc_start: 0.8038 (mp10) cc_final: 0.7414 (mp10) REVERT: B 567 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7672 (mpp80) REVERT: B 737 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: C 267 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: C 393 ASP cc_start: 0.7670 (p0) cc_final: 0.7409 (t0) REVERT: C 427 MET cc_start: 0.8521 (tpp) cc_final: 0.8222 (tpt) REVERT: C 678 MET cc_start: 0.7669 (mmm) cc_final: 0.6476 (mmp) REVERT: D 267 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: D 427 MET cc_start: 0.7764 (tpt) cc_final: 0.7219 (tpp) REVERT: D 465 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6781 (mmm160) REVERT: D 730 GLU cc_start: 0.7372 (pt0) cc_final: 0.7014 (pm20) REVERT: D 737 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: E 421 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: E 427 MET cc_start: 0.8628 (tpp) cc_final: 0.8348 (tpp) REVERT: E 567 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7593 (mpp80) REVERT: E 678 MET cc_start: 0.7368 (mmm) cc_final: 0.6383 (mmp) REVERT: E 730 GLU cc_start: 0.7444 (pt0) cc_final: 0.7100 (pm20) REVERT: F 349 ARG cc_start: 0.8930 (ttm170) cc_final: 0.8623 (tpm170) REVERT: F 368 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8342 (p0) REVERT: F 397 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: F 427 MET cc_start: 0.8576 (tpp) cc_final: 0.8160 (tpp) REVERT: F 465 ARG cc_start: 0.6979 (mmt90) cc_final: 0.6590 (mmm160) REVERT: F 678 MET cc_start: 0.8169 (tpp) cc_final: 0.7483 (mmp) REVERT: F 730 GLU cc_start: 0.7615 (pt0) cc_final: 0.7126 (pm20) REVERT: F 757 MET cc_start: 0.8929 (mmm) cc_final: 0.8661 (tpp) outliers start: 91 outliers final: 76 residues processed: 365 average time/residue: 0.4153 time to fit residues: 246.1524 Evaluate side-chains 362 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 274 time to evaluate : 3.740 ------------------------------------------------------------------------------- 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 265 PHE 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 484 ASP Chi-restraints excluded: chain A residue 492 LEU 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 599 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 683 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 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 469 VAL 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 606 THR Chi-restraints excluded: chain B residue 613 THR 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 205 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 267 PHE 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 497 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 464 LEU 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 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL 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 467 THR Chi-restraints excluded: chain E residue 469 VAL 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 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 368 ASP Chi-restraints excluded: chain F residue 397 GLU 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 497 VAL Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 418 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 390 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 404 HIS C 404 HIS D 296 ASN D 404 HIS 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 = 0.4413 r_free = 0.4413 target = 0.171466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.124822 restraints weight = 63596.129| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 4.29 r_work: 0.3662 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31775 Z= 0.119 Angle : 0.568 10.661 43163 Z= 0.286 Chirality : 0.045 0.134 5054 Planarity : 0.004 0.056 5846 Dihedral : 4.075 54.012 4716 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.47 % Allowed : 25.50 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4446 helix: 1.25 (0.13), residues: 1806 sheet: -0.74 (0.28), residues: 402 loop : -2.09 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 454 HIS 0.004 0.001 HIS C 226 PHE 0.025 0.001 PHE B 674 TYR 0.023 0.001 TYR E 203 ARG 0.004 0.000 ARG F 322 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1254) hydrogen bonds : angle 4.43444 ( 3558) covalent geometry : bond 0.00280 (31775) covalent geometry : angle 0.56799 (43163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18909.45 seconds wall clock time: 325 minutes 28.73 seconds (19528.73 seconds total)