Starting phenix.real_space_refine on Fri Jul 26 01:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_19473.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_19473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_19473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_19473.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rs9_19473/07_2024/8rs9_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 Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C GLU 756": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E GLU 607": "OE1" <-> "OE2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 556": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F GLU 737": "OE1" <-> "OE2" Time to flip residues: 0.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 16.29, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 12.31 Conformation dependent library (CDL) restraints added in 6.0 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: 3.67 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: 10.73 Time building geometry restraints manager: 13.48 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: 99.11 - 106.10: 790 106.10 - 113.09: 17048 113.09 - 120.07: 11336 120.07 - 127.06: 13734 127.06 - 134.05: 255 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 2.520 nonbonded pdb=" NH2 ARG A 465 " pdb=" OE2 GLU B 607 " model vdw 2.051 2.520 nonbonded pdb=" OD1 ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.060 2.440 nonbonded pdb=" OD1 ASP E 307 " pdb=" OG SER E 352 " model vdw 2.070 2.440 nonbonded pdb=" O GLU B 546 " pdb=" OG1 THR B 549 " model vdw 2.087 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 78.320 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.130 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.600 ------------------------------------------------------------------------------- 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= 0.211 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 650 time to evaluate : 3.578 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: 0.4867 time to fit residues: 475.8670 Evaluate side-chains 294 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 3.875 ------------------------------------------------------------------------------- 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: 40.0000 chunk 336 optimal weight: 20.0000 chunk 186 optimal weight: 0.0770 chunk 114 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 chunk 179 optimal weight: 0.2980 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 403 optimal weight: 1.9990 overall best weight: 3.0744 ------------------------------------------------------------------------------- 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 ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 494 GLN C 260 ASN C 494 GLN C 660 ASN D 616 ASN D 660 ASN D 680 ASN E 260 ASN E 404 HIS E 460 ASN E 641 GLN F 382 GLN F 558 ASN F 568 GLN F 660 ASN F 680 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31775 Z= 0.243 Angle : 0.662 9.688 43163 Z= 0.343 Chirality : 0.046 0.157 5054 Planarity : 0.005 0.055 5846 Dihedral : 4.922 56.915 4718 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.74 % Allowed : 22.55 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.13), residues: 4446 helix: 0.67 (0.12), residues: 1770 sheet: -0.87 (0.28), residues: 432 loop : -2.54 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 454 HIS 0.008 0.001 HIS C 226 PHE 0.017 0.002 PHE E 736 TYR 0.014 0.001 TYR B 203 ARG 0.008 0.001 ARG A 732 *********************** 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 435 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 305 time to evaluate : 3.773 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: A 709 ARG cc_start: 0.8214 (mpt-90) cc_final: 0.7237 (ptm-80) REVERT: B 322 ARG cc_start: 0.6410 (mpt180) cc_final: 0.5936 (mpt180) REVERT: C 550 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6775 (mtm) REVERT: D 709 ARG cc_start: 0.8171 (mpt-90) cc_final: 0.7149 (ptm-80) REVERT: E 362 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6829 (mtt90) REVERT: E 397 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: E 709 ARG cc_start: 0.7962 (mpt-90) cc_final: 0.7035 (ptm-80) REVERT: F 362 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7157 (mtt180) outliers start: 130 outliers final: 66 residues processed: 420 average time/residue: 0.4149 time to fit residues: 276.5158 Evaluate side-chains 326 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 256 time to evaluate : 3.751 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain 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 285 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 410 ASP 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 550 MET Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 GLN Chi-restraints excluded: chain E residue 410 ASP 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 F residue 205 ASP Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 362 ARG Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 664 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 40.0000 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 403 optimal weight: 0.6980 chunk 436 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 400 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 660 ASN C 260 ASN C 443 ASN C 680 ASN D 404 HIS D 660 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 404 HIS E 443 ASN E 490 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 660 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3106 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= 0.216 Angle : 0.583 8.919 43163 Z= 0.303 Chirality : 0.045 0.144 5054 Planarity : 0.004 0.051 5846 Dihedral : 4.585 59.056 4716 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.74 % Allowed : 22.80 % Favored : 72.46 % 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: -1.18 (0.13), residues: 4446 helix: 0.86 (0.12), residues: 1812 sheet: -0.82 (0.27), residues: 492 loop : -2.32 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 454 HIS 0.004 0.001 HIS F 226 PHE 0.023 0.001 PHE F 265 TYR 0.017 0.001 TYR B 203 ARG 0.010 0.001 ARG B 599 *********************** 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 413 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 283 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 709 ARG cc_start: 0.8294 (mpt-90) cc_final: 0.7269 (ptm-80) REVERT: B 567 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6919 (mpp80) REVERT: B 709 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7141 (ptm-80) REVERT: B 737 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: C 550 MET cc_start: 0.7055 (mtt) cc_final: 0.6806 (mtm) REVERT: D 709 ARG cc_start: 0.8242 (mpt-90) cc_final: 0.7180 (ptm-80) REVERT: E 362 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6851 (mtt90) REVERT: E 397 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: E 421 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: E 476 TRP cc_start: 0.6601 (OUTLIER) cc_final: 0.5130 (m100) REVERT: E 709 ARG cc_start: 0.7870 (mpt-90) cc_final: 0.6992 (ptm-80) outliers start: 130 outliers final: 69 residues processed: 401 average time/residue: 0.4100 time to fit residues: 264.2691 Evaluate side-chains 331 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 255 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP 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 673 GLU 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 285 ASN Chi-restraints excluded: chain B residue 364 ASP 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 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 680 ASN 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 285 ASN Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 414 LEU 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 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.9990 chunk 303 optimal weight: 50.0000 chunk 209 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 429 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 384 optimal weight: 50.0000 chunk 115 optimal weight: 0.0970 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 494 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 404 HIS C 460 ASN D 404 HIS D 660 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 404 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN F 404 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31775 Z= 0.277 Angle : 0.629 8.555 43163 Z= 0.323 Chirality : 0.047 0.215 5054 Planarity : 0.005 0.057 5846 Dihedral : 4.578 58.768 4716 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.36 % Allowed : 23.28 % 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: -1.28 (0.13), residues: 4446 helix: 0.74 (0.12), residues: 1824 sheet: -1.21 (0.26), residues: 516 loop : -2.27 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 454 HIS 0.007 0.002 HIS D 226 PHE 0.025 0.002 PHE F 265 TYR 0.021 0.002 TYR C 203 ARG 0.006 0.001 ARG C 599 *********************** 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 425 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 278 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 564 ASP cc_start: 0.8090 (t70) cc_final: 0.7845 (t0) REVERT: B 567 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7097 (mpp80) REVERT: B 737 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: C 267 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: C 465 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7129 (mmm160) REVERT: D 349 ARG cc_start: 0.8121 (tpm170) cc_final: 0.7900 (tpm170) REVERT: D 674 PHE cc_start: 0.5967 (t80) cc_final: 0.5709 (t80) REVERT: D 678 MET cc_start: 0.8171 (mmm) cc_final: 0.7534 (mmm) REVERT: D 737 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: E 362 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7075 (mtt90) REVERT: E 397 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: E 421 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: E 567 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7138 (mpp80) REVERT: E 709 ARG cc_start: 0.7775 (mpt-90) cc_final: 0.6893 (ttp80) REVERT: F 388 MET cc_start: 0.6849 (mmp) cc_final: 0.6573 (mmm) outliers start: 147 outliers final: 88 residues processed: 415 average time/residue: 0.4121 time to fit residues: 276.9243 Evaluate side-chains 342 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 245 time to evaluate : 3.437 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 680 ASN 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 285 ASN Chi-restraints excluded: chain C residue 410 ASP 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 492 LEU Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 673 GLU Chi-restraints excluded: chain D residue 699 ILE 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 362 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 476 TRP Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 410 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 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 613 THR Chi-restraints excluded: chain F residue 680 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 319 optimal weight: 6.9990 chunk 177 optimal weight: 0.0170 chunk 366 optimal weight: 9.9990 chunk 296 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 219 optimal weight: 10.0000 chunk 385 optimal weight: 50.0000 chunk 108 optimal weight: 1.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- 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 ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 660 ASN C 404 HIS D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 494 GLN E 660 ASN F 260 ASN F 404 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31775 Z= 0.285 Angle : 0.621 9.218 43163 Z= 0.319 Chirality : 0.047 0.323 5054 Planarity : 0.005 0.058 5846 Dihedral : 4.558 59.492 4716 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.14 % Allowed : 24.41 % Favored : 70.45 % 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: -1.31 (0.13), residues: 4446 helix: 0.74 (0.12), residues: 1818 sheet: -1.29 (0.25), residues: 516 loop : -2.28 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 476 HIS 0.007 0.001 HIS C 226 PHE 0.027 0.001 PHE F 265 TYR 0.018 0.002 TYR C 203 ARG 0.008 0.000 ARG B 599 *********************** 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 406 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 265 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: A 599 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.4978 (mtp85) REVERT: A 678 MET cc_start: 0.8228 (tpp) cc_final: 0.7559 (mmp) REVERT: B 427 MET cc_start: 0.8539 (tpp) cc_final: 0.8231 (tpp) REVERT: B 564 ASP cc_start: 0.8103 (t70) cc_final: 0.7846 (t0) REVERT: B 567 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7204 (mpp80) REVERT: B 737 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: C 267 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: C 397 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: C 427 MET cc_start: 0.8438 (tpp) cc_final: 0.8177 (tpp) REVERT: C 465 ARG cc_start: 0.7636 (mmt90) cc_final: 0.7201 (mmm160) REVERT: D 349 ARG cc_start: 0.8118 (tpm170) cc_final: 0.7891 (tpm170) REVERT: D 674 PHE cc_start: 0.6149 (t80) cc_final: 0.5831 (t80) REVERT: D 678 MET cc_start: 0.8138 (mmm) cc_final: 0.7270 (mmp) REVERT: D 709 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.7218 (ptm-80) REVERT: D 737 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: E 362 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7053 (mtt90) REVERT: E 397 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: E 421 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: E 567 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7249 (mpp80) outliers start: 141 outliers final: 102 residues processed: 390 average time/residue: 0.4026 time to fit residues: 255.6485 Evaluate side-chains 360 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 247 time to evaluate : 3.181 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR 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 574 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 761 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 285 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 527 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 680 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 720 MET 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 285 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 410 ASP 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 535 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 680 ASN 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 362 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP 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 534 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 410 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 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 601 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 680 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 0.9980 chunk 386 optimal weight: 30.0000 chunk 84 optimal weight: 0.0070 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 429 optimal weight: 0.7980 chunk 356 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 225 optimal weight: 50.0000 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 533 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 660 ASN F 404 HIS F 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31775 Z= 0.205 Angle : 0.576 8.964 43163 Z= 0.291 Chirality : 0.045 0.135 5054 Planarity : 0.004 0.056 5846 Dihedral : 4.373 59.260 4716 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.27 % Allowed : 26.16 % Favored : 69.57 % 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: -1.07 (0.13), residues: 4446 helix: 1.03 (0.13), residues: 1812 sheet: -1.17 (0.25), residues: 516 loop : -2.24 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 454 HIS 0.005 0.001 HIS E 404 PHE 0.025 0.001 PHE F 265 TYR 0.019 0.001 TYR C 203 ARG 0.004 0.000 ARG C 599 *********************** 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 390 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 273 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 599 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.4878 (mtp85) REVERT: A 678 MET cc_start: 0.8121 (tpp) cc_final: 0.7337 (mmp) REVERT: B 564 ASP cc_start: 0.8082 (t70) cc_final: 0.7832 (t0) REVERT: B 567 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7262 (mpp80) REVERT: B 737 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: C 267 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: C 465 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7188 (mmm160) REVERT: D 349 ARG cc_start: 0.8115 (tpm170) cc_final: 0.7861 (tpm170) REVERT: D 678 MET cc_start: 0.8082 (mmm) cc_final: 0.7231 (mmp) REVERT: D 737 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: E 362 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7040 (mtt90) REVERT: E 397 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: E 421 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: E 567 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7136 (mpp80) REVERT: E 677 LYS cc_start: 0.7270 (pttp) cc_final: 0.7041 (mmmt) REVERT: F 388 MET cc_start: 0.7031 (mmp) cc_final: 0.6608 (mmm) outliers start: 117 outliers final: 85 residues processed: 378 average time/residue: 0.3968 time to fit residues: 247.1560 Evaluate side-chains 350 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 255 time to evaluate : 3.622 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 535 CYS 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 680 ASN Chi-restraints excluded: chain A residue 720 MET 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 285 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 720 MET 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 410 ASP 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 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 680 ASN Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 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 362 ARG Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP 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 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 680 ASN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 313 optimal weight: 0.0050 chunk 243 optimal weight: 8.9990 chunk 361 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 558 ASN B 602 ASN B 660 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 660 ASN F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31775 Z= 0.163 Angle : 0.551 9.896 43163 Z= 0.278 Chirality : 0.044 0.179 5054 Planarity : 0.004 0.054 5846 Dihedral : 4.130 58.315 4714 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.01 % Allowed : 27.58 % Favored : 68.41 % 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: -0.80 (0.13), residues: 4446 helix: 1.18 (0.13), residues: 1860 sheet: -0.37 (0.27), residues: 432 loop : -2.23 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 454 HIS 0.003 0.001 HIS D 404 PHE 0.025 0.001 PHE C 674 TYR 0.018 0.001 TYR C 203 ARG 0.004 0.000 ARG B 599 *********************** 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 396 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 286 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.4776 (mtp85) REVERT: A 674 PHE cc_start: 0.5674 (t80) cc_final: 0.5313 (t80) REVERT: A 678 MET cc_start: 0.8007 (tpp) cc_final: 0.7248 (mmt) REVERT: B 322 ARG cc_start: 0.6380 (mpt180) cc_final: 0.5974 (mpt180) REVERT: B 427 MET cc_start: 0.8621 (tpp) cc_final: 0.8327 (tpp) REVERT: B 564 ASP cc_start: 0.8054 (t70) cc_final: 0.7800 (t0) REVERT: B 567 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7195 (mpp80) REVERT: B 737 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: C 267 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: C 465 ARG cc_start: 0.7708 (mmt90) cc_final: 0.7061 (mmm160) REVERT: D 349 ARG cc_start: 0.8118 (tpm170) cc_final: 0.7845 (tpm170) REVERT: D 427 MET cc_start: 0.8593 (tpp) cc_final: 0.8162 (tpp) REVERT: D 550 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5944 (mtp) REVERT: D 678 MET cc_start: 0.7993 (mmm) cc_final: 0.7140 (mmp) REVERT: D 737 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: E 362 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6960 (mtt90) REVERT: E 397 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: E 421 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: E 458 GLN cc_start: 0.7821 (mp10) cc_final: 0.7597 (mp10) REVERT: E 567 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7186 (mpp80) REVERT: E 678 MET cc_start: 0.7387 (mmm) cc_final: 0.6636 (mmp) outliers start: 110 outliers final: 76 residues processed: 380 average time/residue: 0.4219 time to fit residues: 260.1101 Evaluate side-chains 348 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 262 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 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 680 ASN Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 720 MET 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 410 ASP 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 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 601 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 362 ARG Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 255 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 40.0000 chunk 272 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 602 ASN B 660 ASN D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 660 ASN F 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31775 Z= 0.224 Angle : 0.587 9.744 43163 Z= 0.296 Chirality : 0.045 0.139 5054 Planarity : 0.004 0.054 5846 Dihedral : 4.160 58.102 4714 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 4.52 % Allowed : 27.18 % Favored : 68.30 % 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: -0.86 (0.13), residues: 4446 helix: 1.12 (0.12), residues: 1860 sheet: -0.45 (0.27), residues: 432 loop : -2.23 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 454 HIS 0.006 0.001 HIS A 226 PHE 0.024 0.001 PHE F 265 TYR 0.017 0.001 TYR C 203 ARG 0.007 0.000 ARG C 599 *********************** 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 384 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 260 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.4983 (mtp85) REVERT: A 678 MET cc_start: 0.8062 (tpp) cc_final: 0.7291 (mmp) REVERT: B 427 MET cc_start: 0.8531 (tpp) cc_final: 0.8104 (tpp) REVERT: B 564 ASP cc_start: 0.8069 (t70) cc_final: 0.7827 (t0) REVERT: B 567 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7320 (mpp80) REVERT: B 737 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: C 267 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: C 427 MET cc_start: 0.8419 (tpp) cc_final: 0.8187 (tpp) REVERT: C 465 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7530 (mmm160) REVERT: C 535 CYS cc_start: 0.7369 (t) cc_final: 0.7101 (t) REVERT: D 349 ARG cc_start: 0.8105 (tpm170) cc_final: 0.7851 (tpm170) REVERT: D 427 MET cc_start: 0.8529 (tpp) cc_final: 0.8310 (tpp) REVERT: D 678 MET cc_start: 0.8099 (mmm) cc_final: 0.7242 (mmp) REVERT: D 737 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: E 362 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7078 (mtt90) REVERT: E 397 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: E 421 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: E 427 MET cc_start: 0.8489 (tpp) cc_final: 0.8058 (tpp) REVERT: E 458 GLN cc_start: 0.7884 (mp10) cc_final: 0.7584 (mp10) REVERT: E 567 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7196 (mpp80) REVERT: E 678 MET cc_start: 0.7525 (mmm) cc_final: 0.7100 (mmm) outliers start: 124 outliers final: 90 residues processed: 372 average time/residue: 0.3986 time to fit residues: 242.2662 Evaluate side-chains 355 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 256 time to evaluate : 3.716 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 680 ASN 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 285 ASN Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 720 MET 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 285 ASN Chi-restraints excluded: chain C residue 410 ASP 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 451 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 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 362 ARG Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP 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 534 GLU 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 680 ASN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 601 ILE 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 389 optimal weight: 4.9990 chunk 409 optimal weight: 10.0000 chunk 374 optimal weight: 40.0000 chunk 398 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 377 optimal weight: 50.0000 chunk 397 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 260 ASN B 404 HIS B 660 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31775 Z= 0.336 Angle : 0.662 13.398 43163 Z= 0.337 Chirality : 0.048 0.195 5054 Planarity : 0.005 0.057 5846 Dihedral : 4.460 56.403 4714 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.60 % Allowed : 27.03 % Favored : 68.37 % 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: -1.22 (0.13), residues: 4446 helix: 0.91 (0.13), residues: 1734 sheet: -0.89 (0.27), residues: 402 loop : -2.26 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 454 HIS 0.008 0.001 HIS A 226 PHE 0.027 0.002 PHE F 265 TYR 0.017 0.001 TYR C 203 ARG 0.010 0.001 ARG C 599 *********************** 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 374 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 248 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5138 (mtp85) REVERT: A 678 MET cc_start: 0.8158 (tpp) cc_final: 0.7749 (tpp) REVERT: B 219 MET cc_start: 0.8739 (mtp) cc_final: 0.7894 (ttm) REVERT: B 564 ASP cc_start: 0.8117 (t70) cc_final: 0.7883 (t0) REVERT: B 567 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7423 (mpp80) REVERT: B 737 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: C 267 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: C 388 MET cc_start: 0.7001 (mmp) cc_final: 0.6533 (mmm) REVERT: C 427 MET cc_start: 0.8508 (tpp) cc_final: 0.8269 (tpp) REVERT: C 535 CYS cc_start: 0.7485 (t) cc_final: 0.7283 (t) REVERT: D 427 MET cc_start: 0.8576 (tpp) cc_final: 0.8338 (tpp) REVERT: D 678 MET cc_start: 0.8256 (mmm) cc_final: 0.7175 (mmp) REVERT: D 737 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: E 219 MET cc_start: 0.8827 (mtp) cc_final: 0.7982 (ttm) REVERT: E 362 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7085 (mtt90) REVERT: E 397 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: E 421 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: E 427 MET cc_start: 0.8453 (tpp) cc_final: 0.7973 (tpp) REVERT: E 567 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7230 (mpp80) REVERT: E 678 MET cc_start: 0.7722 (mmm) cc_final: 0.7376 (mmm) REVERT: F 427 MET cc_start: 0.7569 (tpt) cc_final: 0.7269 (tpp) REVERT: F 674 PHE cc_start: 0.5486 (t80) cc_final: 0.5229 (t80) REVERT: F 678 MET cc_start: 0.8178 (tpp) cc_final: 0.7452 (mmp) outliers start: 126 outliers final: 92 residues processed: 362 average time/residue: 0.4014 time to fit residues: 238.9950 Evaluate side-chains 336 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 235 time to evaluate : 3.595 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR 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 613 THR Chi-restraints excluded: chain A residue 680 ASN 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 285 ASN Chi-restraints excluded: chain B residue 410 ASP 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 527 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 680 ASN 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 410 ASP 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 451 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR 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 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 680 ASN 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 362 ARG Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 410 ASP 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 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 410 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 442 optimal weight: 0.0970 chunk 407 optimal weight: 0.0370 chunk 352 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 404 HIS B 660 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5071 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= 0.200 Angle : 0.590 9.503 43163 Z= 0.296 Chirality : 0.045 0.165 5054 Planarity : 0.004 0.052 5846 Dihedral : 4.250 56.174 4714 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.47 % Allowed : 27.87 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.13), residues: 4446 helix: 1.13 (0.13), residues: 1788 sheet: -0.68 (0.27), residues: 438 loop : -2.26 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 454 HIS 0.004 0.001 HIS C 226 PHE 0.024 0.001 PHE F 265 TYR 0.017 0.001 TYR C 203 ARG 0.006 0.000 ARG A 625 ********************** 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 356 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 261 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 LYS cc_start: 0.8105 (mttp) cc_final: 0.7612 (mtmm) REVERT: A 599 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5107 (mtp85) REVERT: A 678 MET cc_start: 0.8020 (tpp) cc_final: 0.7320 (mmp) REVERT: B 219 MET cc_start: 0.8620 (mtp) cc_final: 0.7976 (ttm) REVERT: B 427 MET cc_start: 0.8648 (tpp) cc_final: 0.8195 (tpp) REVERT: B 564 ASP cc_start: 0.8076 (t70) cc_final: 0.7813 (t0) REVERT: B 567 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7375 (mpp80) REVERT: B 678 MET cc_start: 0.7895 (tpp) cc_final: 0.7362 (mmp) REVERT: B 737 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: C 267 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: C 427 MET cc_start: 0.8485 (tpp) cc_final: 0.8233 (tpp) REVERT: C 584 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7262 (mtmm) REVERT: D 349 ARG cc_start: 0.8141 (tpm170) cc_final: 0.7877 (tpm170) REVERT: D 427 MET cc_start: 0.8554 (tpp) cc_final: 0.8262 (tpp) REVERT: D 674 PHE cc_start: 0.5252 (t80) cc_final: 0.4943 (t80) REVERT: D 678 MET cc_start: 0.8137 (mmm) cc_final: 0.7124 (mmt) REVERT: D 737 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: E 219 MET cc_start: 0.8687 (mtp) cc_final: 0.8036 (ttm) REVERT: E 362 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7066 (mtt90) REVERT: E 397 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: E 421 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: E 427 MET cc_start: 0.8438 (tpp) cc_final: 0.7942 (tpp) REVERT: E 458 GLN cc_start: 0.7894 (mp10) cc_final: 0.7570 (mp10) REVERT: E 567 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7244 (mpp80) REVERT: E 678 MET cc_start: 0.7640 (mmm) cc_final: 0.7260 (mmm) REVERT: F 674 PHE cc_start: 0.5357 (t80) cc_final: 0.5105 (t80) REVERT: F 678 MET cc_start: 0.8099 (tpp) cc_final: 0.7382 (mmp) outliers start: 95 outliers final: 83 residues processed: 352 average time/residue: 0.4012 time to fit residues: 230.3380 Evaluate side-chains 345 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 253 time to evaluate : 3.729 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR 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 613 THR Chi-restraints excluded: chain A residue 680 ASN 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 285 ASN 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 664 SER Chi-restraints excluded: chain B residue 680 ASN 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 410 ASP 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 451 ASP 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 D residue 205 ASP Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 680 ASN 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 362 ARG 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 469 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain F residue 410 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 40.0000 chunk 375 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 660 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.167457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.123127 restraints weight = 64553.544| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.93 r_work: 0.3663 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5162 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= 0.184 Angle : 0.576 10.125 43163 Z= 0.288 Chirality : 0.045 0.164 5054 Planarity : 0.004 0.052 5846 Dihedral : 4.086 55.655 4714 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.43 % Allowed : 27.84 % Favored : 68.73 % 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: -0.82 (0.13), residues: 4446 helix: 1.22 (0.13), residues: 1800 sheet: -0.39 (0.26), residues: 468 loop : -2.22 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 454 HIS 0.004 0.001 HIS A 226 PHE 0.024 0.001 PHE A 674 TYR 0.017 0.001 TYR C 203 ARG 0.004 0.000 ARG C 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7038.92 seconds wall clock time: 124 minutes 59.36 seconds (7499.36 seconds total)