Starting phenix.real_space_refine on Mon Aug 25 18:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3ja8_6338/08_2025/3ja8_6338.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.058 sd= 0.697 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 18734 2.51 5 N 5233 2.21 5 O 5727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29838 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 558} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4745 Classifications: {'peptide': 605} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 558} Chain breaks: 4 Chain: "4" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5081 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 17, 'PTRANS': 23, 'TRANS': 599} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 4962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4962 Classifications: {'peptide': 633} Link IDs: {'CIS': 18, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 587} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 4742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4742 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 29, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 564} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 20, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 638} Chain breaks: 3 Chain: "2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.16, per 1000 atoms: 0.21 Number of scatterers: 29838 At special positions: 0 Unit cell: (149.16, 138.6, 149.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 12 15.00 O 5727 8.00 N 5233 7.00 C 18734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 211 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 236 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 834.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 36 sheets defined 40.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain '2' and resid 203 through 217 removed outlier: 4.001A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU 2 210 " --> pdb=" O THR 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 237 removed outlier: 4.271A pdb=" N GLU 2 236 " --> pdb=" O ARG 2 232 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET 2 237 " --> pdb=" O THR 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 removed outlier: 3.626A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS 2 253 " --> pdb=" O LEU 2 249 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 262 removed outlier: 3.907A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.919A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 removed outlier: 3.543A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '2' and resid 477 through 486 removed outlier: 4.346A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 502 removed outlier: 4.196A pdb=" N ALA 2 502 " --> pdb=" O ILE 2 498 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 3.817A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 2 515 " --> pdb=" O ILE 2 511 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 4.459A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 609 through 612 Processing helix chain '2' and resid 613 through 627 removed outlier: 4.038A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 676 removed outlier: 3.771A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 705 removed outlier: 3.560A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 4.181A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 784 through 799 removed outlier: 3.735A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.046A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.812A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 858 removed outlier: 3.768A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 27 Processing helix chain '3' and resid 29 through 34 Processing helix chain '3' and resid 36 through 60 removed outlier: 3.976A pdb=" N ASP 3 40 " --> pdb=" O THR 3 36 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN 3 57 " --> pdb=" O ALA 3 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP 3 59 " --> pdb=" O ASN 3 55 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN 3 60 " --> pdb=" O TYR 3 56 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 107 removed outlier: 4.403A pdb=" N LEU 3 103 " --> pdb=" O SER 3 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG 3 104 " --> pdb=" O LEU 3 100 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU 3 105 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix removed outlier: 4.354A pdb=" N ASP 3 137 " --> pdb=" O ALA 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 344 through 354 removed outlier: 3.785A pdb=" N ARG 3 348 " --> pdb=" O ASP 3 344 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 removed outlier: 3.812A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 479 through 491 removed outlier: 3.877A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 543 removed outlier: 3.585A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 569 removed outlier: 4.115A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 removed outlier: 3.564A pdb=" N LEU 3 656 " --> pdb=" O THR 3 652 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 675 through 694 removed outlier: 3.526A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.796A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 189 through 200 removed outlier: 3.975A pdb=" N PHE 4 197 " --> pdb=" O ASN 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 209 removed outlier: 3.824A pdb=" N ILE 4 208 " --> pdb=" O LYS 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 removed outlier: 4.417A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 4.316A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 Processing helix chain '4' and resid 294 through 299 removed outlier: 4.157A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 Processing helix chain '4' and resid 478 through 483 removed outlier: 3.728A pdb=" N GLU 4 482 " --> pdb=" O THR 4 478 " (cutoff:3.500A) Processing helix chain '4' and resid 483 through 488 Processing helix chain '4' and resid 502 through 513 removed outlier: 3.930A pdb=" N LEU 4 506 " --> pdb=" O THR 4 502 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU 4 511 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) Processing helix chain '4' and resid 514 through 516 No H-bonds generated for 'chain '4' and resid 514 through 516' Processing helix chain '4' and resid 517 through 527 removed outlier: 3.920A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.555A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.869A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.030A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 692 Processing helix chain '4' and resid 695 through 702 removed outlier: 3.798A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 716 through 725 Processing helix chain '4' and resid 745 through 758 removed outlier: 3.559A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 766 through 779 removed outlier: 3.530A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 821 through 835 removed outlier: 3.616A pdb=" N ALA 4 825 " --> pdb=" O ASP 4 821 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 37 removed outlier: 3.521A pdb=" N PHE 5 31 " --> pdb=" O ILE 5 27 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 removed outlier: 4.023A pdb=" N ASP 5 48 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 4.021A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 108 Proline residue: 5 88 - end of helix removed outlier: 3.941A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 removed outlier: 3.804A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 350 through 361 removed outlier: 3.761A pdb=" N GLU 5 354 " --> pdb=" O THR 5 350 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 371 Processing helix chain '5' and resid 381 through 393 removed outlier: 4.103A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 433 removed outlier: 3.869A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 removed outlier: 3.676A pdb=" N LEU 5 471 " --> pdb=" O GLY 5 467 " (cutoff:3.500A) Processing helix chain '5' and resid 487 through 500 removed outlier: 3.722A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 5 499 " --> pdb=" O GLU 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 529 through 534 Processing helix chain '5' and resid 544 through 550 Processing helix chain '5' and resid 561 through 577 removed outlier: 3.972A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 592 Processing helix chain '5' and resid 596 through 610 removed outlier: 3.654A pdb=" N LYS 5 600 " --> pdb=" O ILE 5 596 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS 5 610 " --> pdb=" O CYS 5 606 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 637 Processing helix chain '5' and resid 638 through 640 No H-bonds generated for 'chain '5' and resid 638 through 640' Processing helix chain '5' and resid 649 through 667 removed outlier: 3.571A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 4.068A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER 5 693 " --> pdb=" O MET 5 689 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 121 Processing helix chain '6' and resid 135 through 147 removed outlier: 3.784A pdb=" N GLN 6 139 " --> pdb=" O VAL 6 135 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 162 removed outlier: 4.329A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 193 removed outlier: 3.812A pdb=" N GLN 6 173 " --> pdb=" O ALA 6 169 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR 6 175 " --> pdb=" O SER 6 171 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG 6 176 " --> pdb=" O GLU 6 172 " (cutoff:3.500A) Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 275 through 279 Processing helix chain '6' and resid 511 through 522 removed outlier: 4.193A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 541 through 552 removed outlier: 4.091A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN 6 550 " --> pdb=" O GLY 6 546 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.044A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 644 Processing helix chain '6' and resid 646 through 658 removed outlier: 3.908A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 720 through 736 Processing helix chain '6' and resid 749 through 759 removed outlier: 3.932A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 783 removed outlier: 3.655A pdb=" N LEU 6 773 " --> pdb=" O ALA 6 769 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 6 774 " --> pdb=" O ARG 6 770 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 6 782 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.711A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 837 removed outlier: 3.559A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 25 removed outlier: 3.747A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 93 Processing helix chain '7' and resid 102 through 108 removed outlier: 3.918A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 124 removed outlier: 4.065A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 165 removed outlier: 3.675A pdb=" N LEU 7 143 " --> pdb=" O LEU 7 139 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU 7 154 " --> pdb=" O ASN 7 150 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER 7 163 " --> pdb=" O ASN 7 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 7 164 " --> pdb=" O GLU 7 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 178 through 189 removed outlier: 3.765A pdb=" N ARG 7 182 " --> pdb=" O ASN 7 178 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR 7 189 " --> pdb=" O VAL 7 185 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 197 Processing helix chain '7' and resid 210 through 214 Processing helix chain '7' and resid 336 through 340 removed outlier: 3.926A pdb=" N LEU 7 339 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL 7 340 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 336 through 340' Processing helix chain '7' and resid 363 through 367 removed outlier: 3.564A pdb=" N LYS 7 367 " --> pdb=" O LYS 7 364 " (cutoff:3.500A) Processing helix chain '7' and resid 397 through 407 removed outlier: 3.633A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 Processing helix chain '7' and resid 425 through 438 removed outlier: 4.094A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 477 Processing helix chain '7' and resid 489 through 494 Processing helix chain '7' and resid 531 through 540 Processing helix chain '7' and resid 541 through 543 No H-bonds generated for 'chain '7' and resid 541 through 543' Processing helix chain '7' and resid 587 through 592 removed outlier: 3.564A pdb=" N LEU 7 591 " --> pdb=" O PRO 7 587 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER 7 592 " --> pdb=" O ALA 7 588 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 587 through 592' Processing helix chain '7' and resid 605 through 622 removed outlier: 3.761A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 Processing helix chain '7' and resid 653 through 674 removed outlier: 3.507A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.938A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 3.565A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) Processing helix chain '7' and resid 725 through 729 removed outlier: 3.654A pdb=" N TYR 7 728 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 7 729 " --> pdb=" O SER 7 726 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 725 through 729' Processing sheet with id=A, first strand: chain '2' and resid 241 through 242 removed outlier: 3.582A pdb=" N LEU 2 242 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain '2' and resid 351 through 352 removed outlier: 4.033A pdb=" N LYS 2 335 " --> pdb=" O VAL 2 381 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU 2 411 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LYS 2 457 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain '2' and resid 563 through 565 removed outlier: 6.188A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain '2' and resid 629 through 631 Processing sheet with id=E, first strand: chain '3' and resid 180 through 185 removed outlier: 3.570A pdb=" N LEU 3 320 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain '3' and resid 180 through 185 removed outlier: 4.475A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain '3' and resid 198 through 199 removed outlier: 3.535A pdb=" N ARG 3 212 " --> pdb=" O SER 3 199 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain '3' and resid 201 through 202 Processing sheet with id=I, first strand: chain '3' and resid 391 through 392 removed outlier: 4.015A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain '3' and resid 431 through 433 removed outlier: 7.103A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain '3' and resid 494 through 497 Processing sheet with id=L, first strand: chain '4' and resid 325 through 327 Processing sheet with id=M, first strand: chain '4' and resid 339 through 344 removed outlier: 6.764A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain '4' and resid 348 through 349 Processing sheet with id=O, first strand: chain '4' and resid 397 through 400 Processing sheet with id=P, first strand: chain '4' and resid 590 through 591 removed outlier: 3.703A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain '4' and resid 606 through 607 Processing sheet with id=R, first strand: chain '4' and resid 653 through 656 Processing sheet with id=S, first strand: chain '5' and resid 60 through 63 removed outlier: 6.194A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=S Processing sheet with id=T, first strand: chain '5' and resid 159 through 168 removed outlier: 7.144A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain '5' and resid 189 through 193 Processing sheet with id=V, first strand: chain '5' and resid 189 through 193 removed outlier: 6.962A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain '5' and resid 436 through 440 removed outlier: 3.844A pdb=" N ASP 5 480 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 5 477 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain '5' and resid 453 through 456 removed outlier: 4.559A pdb=" N ASP 5 456 " --> pdb=" O GLU 5 461 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain '5' and resid 501 through 503 Processing sheet with id=Z, first strand: chain '6' and resid 151 through 154 removed outlier: 6.928A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=Z Processing sheet with id=AA, first strand: chain '6' and resid 455 through 456 removed outlier: 7.359A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR 6 398 " --> pdb=" O HIS 6 458 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS 6 458 " --> pdb=" O THR 6 398 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain '6' and resid 319 through 320 removed outlier: 4.123A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS 6 306 " --> pdb=" O ARG 6 352 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG 6 350 " --> pdb=" O SER 6 308 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain '6' and resid 404 through 405 Processing sheet with id=AD, first strand: chain '6' and resid 570 through 574 removed outlier: 3.580A pdb=" N ILE 6 571 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AF, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AG, first strand: chain '7' and resid 269 through 272 removed outlier: 6.838A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain '7' and resid 299 through 300 removed outlier: 3.924A pdb=" N PHE 7 299 " --> pdb=" O THR 7 261 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP 7 347 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain '7' and resid 481 through 484 removed outlier: 6.604A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN 7 455 " --> pdb=" O ILE 7 596 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE 7 598 " --> pdb=" O ASN 7 455 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain '7' and resid 496 through 498 1090 hydrogen bonds defined for protein. 3114 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: 5.15 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 30019 1.55 - 1.90: 288 1.90 - 2.26: 0 2.26 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 30308 Sorted by residual: bond pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 1.334 2.965 -1.631 1.26e-02 6.30e+03 1.68e+04 bond pdb=" N PRO 3 654 " pdb=" CD PRO 3 654 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" CA VAL 6 560 " pdb=" CB VAL 6 560 " ideal model delta sigma weight residual 1.540 1.593 -0.053 1.36e-02 5.41e+03 1.51e+01 bond pdb=" CA ILE 2 585 " pdb=" CB ILE 2 585 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" CA VAL 3 336 " pdb=" C VAL 3 336 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.27e-02 6.20e+03 1.06e+01 ... (remaining 30303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.77: 40784 6.77 - 13.54: 218 13.54 - 20.31: 5 20.31 - 27.08: 0 27.08 - 33.85: 3 Bond angle restraints: 41010 Sorted by residual: angle pdb=" CA LYS 4 467 " pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 116.33 82.48 33.85 1.32e+00 5.74e-01 6.57e+02 angle pdb=" O LYS 4 467 " pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 123.14 93.75 29.39 1.28e+00 6.10e-01 5.27e+02 angle pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " pdb=" CA VAL 4 469 " ideal model delta sigma weight residual 120.56 91.40 29.16 1.28e+00 6.10e-01 5.19e+02 angle pdb=" C LEU 7 356 " pdb=" N PRO 7 357 " pdb=" CA PRO 7 357 " ideal model delta sigma weight residual 120.14 132.44 -12.30 1.06e+00 8.90e-01 1.35e+02 angle pdb=" N GLY 2 570 " pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " ideal model delta sigma weight residual 114.37 126.42 -12.05 1.26e+00 6.30e-01 9.15e+01 ... (remaining 41005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18282 26.84 - 53.68: 340 53.68 - 80.52: 32 80.52 - 107.36: 6 107.36 - 134.20: 1 Dihedral angle restraints: 18661 sinusoidal: 7585 harmonic: 11076 Sorted by residual: dihedral pdb=" CA GLY 6 600 " pdb=" C GLY 6 600 " pdb=" N LYS 6 601 " pdb=" CA LYS 6 601 " ideal model delta harmonic sigma weight residual 180.00 45.80 134.20 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" CB CYS 5 186 " pdb=" SG CYS 5 186 " pdb=" SG CYS 5 211 " pdb=" CB CYS 5 211 " ideal model delta sinusoidal sigma weight residual 93.00 178.88 -85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CA THR 3 172 " pdb=" C THR 3 172 " pdb=" N ALA 3 173 " pdb=" CA ALA 3 173 " ideal model delta harmonic sigma weight residual 0.00 -44.36 44.36 0 5.00e+00 4.00e-02 7.87e+01 ... (remaining 18658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3972 0.079 - 0.157: 722 0.157 - 0.236: 69 0.236 - 0.314: 6 0.314 - 0.393: 1 Chirality restraints: 4770 Sorted by residual: chirality pdb=" CA GLN 7 209 " pdb=" N GLN 7 209 " pdb=" C GLN 7 209 " pdb=" CB GLN 7 209 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ASN 2 366 " pdb=" N ASN 2 366 " pdb=" C ASN 2 366 " pdb=" CB ASN 2 366 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LYS 7 486 " pdb=" N LYS 7 486 " pdb=" C LYS 7 486 " pdb=" CB LYS 7 486 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4767 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS 4 467 " -0.182 2.00e-02 2.50e+03 2.72e-01 7.39e+02 pdb=" C LYS 4 467 " 0.445 2.00e-02 2.50e+03 pdb=" O LYS 4 467 " -0.253 2.00e-02 2.50e+03 pdb=" N VAL 4 469 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 653 " -0.126 5.00e-02 4.00e+02 1.77e-01 5.00e+01 pdb=" N PRO 3 654 " 0.305 5.00e-02 4.00e+02 pdb=" CA PRO 3 654 " -0.098 5.00e-02 4.00e+02 pdb=" CD PRO 3 654 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 5 18 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO 5 19 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO 5 19 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 5 19 " -0.038 5.00e-02 4.00e+02 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 221 2.38 - 3.01: 19663 3.01 - 3.64: 44463 3.64 - 4.27: 64766 4.27 - 4.90: 105193 Nonbonded interactions: 234306 Sorted by model distance: nonbonded pdb=" OD2 ASP 7 453 " pdb=" OG SER 7 562 " model vdw 1.749 3.040 nonbonded pdb=" OD2 ASP 6 355 " pdb=" N GLY 6 383 " model vdw 1.802 3.120 nonbonded pdb=" NH1 ARG 2 327 " pdb=" OE2 GLU 5 269 " model vdw 1.851 3.120 nonbonded pdb=" O SER 2 298 " pdb=" NH2 ARG 2 319 " model vdw 1.872 3.120 nonbonded pdb=" NZ LYS 5 442 " pdb=" O LYS 5 484 " model vdw 1.919 3.120 ... (remaining 234301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.015 1.631 30315 Z= 1.189 Angle : 1.650 55.285 41020 Z= 1.057 Chirality : 0.060 0.393 4770 Planarity : 0.007 0.272 5273 Dihedral : 10.982 134.195 11452 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.87 % Favored : 91.00 % Rotamer: Outliers : 0.37 % Allowed : 2.47 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 3.21 % Twisted Proline : 0.67 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.10), residues: 3734 helix: -3.37 (0.09), residues: 1282 sheet: -2.01 (0.18), residues: 559 loop : -2.65 (0.11), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 7 73 TYR 0.038 0.003 TYR 3 211 PHE 0.037 0.003 PHE 6 454 TRP 0.034 0.005 TRP 2 589 HIS 0.016 0.002 HIS 4 465 Details of bonding type rmsd covalent geometry : bond 0.01354 (30308) covalent geometry : angle 1.57175 (41010) SS BOND : bond 0.00529 ( 5) SS BOND : angle 32.16596 ( 10) hydrogen bonds : bond 0.16538 ( 1075) hydrogen bonds : angle 9.82086 ( 3114) Misc. bond : bond 0.88448 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 962 time to evaluate : 1.193 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: 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: 2 348 LEU cc_start: 0.7627 (tp) cc_final: 0.7384 (mp) REVERT: 2 698 PHE cc_start: 0.8306 (t80) cc_final: 0.8089 (t80) REVERT: 2 861 PHE cc_start: 0.8007 (m-10) cc_final: 0.7735 (m-10) REVERT: 3 23 ASP cc_start: 0.7983 (t0) cc_final: 0.7733 (t0) REVERT: 3 39 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7541 (ttp-110) REVERT: 3 198 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7206 (ttp-170) REVERT: 3 282 LEU cc_start: 0.8734 (mt) cc_final: 0.8499 (mt) REVERT: 3 365 GLN cc_start: 0.8501 (mt0) cc_final: 0.8148 (mt0) REVERT: 3 524 ASP cc_start: 0.6047 (t0) cc_final: 0.5412 (t0) REVERT: 4 179 ILE cc_start: 0.6981 (tt) cc_final: 0.6739 (tt) REVERT: 4 199 MET cc_start: 0.7691 (mmt) cc_final: 0.7018 (mtp) REVERT: 4 350 ASN cc_start: 0.7609 (m-40) cc_final: 0.7284 (m-40) REVERT: 4 434 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6775 (tm-30) REVERT: 4 444 ILE cc_start: 0.9066 (pp) cc_final: 0.8858 (pt) REVERT: 4 506 LEU cc_start: 0.9236 (mt) cc_final: 0.9023 (mt) REVERT: 5 55 LEU cc_start: 0.7261 (mt) cc_final: 0.6945 (tp) REVERT: 5 99 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8301 (mtpp) REVERT: 5 464 LEU cc_start: 0.8696 (tt) cc_final: 0.8440 (mm) REVERT: 5 478 CYS cc_start: 0.8511 (m) cc_final: 0.8174 (m) REVERT: 5 487 ASP cc_start: 0.7891 (m-30) cc_final: 0.7549 (t0) REVERT: 5 519 VAL cc_start: 0.9409 (t) cc_final: 0.9174 (p) REVERT: 5 621 LYS cc_start: 0.8923 (tptp) cc_final: 0.8647 (tptp) REVERT: 6 133 GLU cc_start: 0.6537 (mp0) cc_final: 0.6197 (mp0) REVERT: 6 139 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7505 (tm-30) REVERT: 6 796 THR cc_start: 0.7884 (m) cc_final: 0.7440 (p) REVERT: 7 122 ASP cc_start: 0.7459 (t0) cc_final: 0.7189 (t0) REVERT: 7 214 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.4826 (tpp-160) REVERT: 7 241 VAL cc_start: 0.8964 (m) cc_final: 0.8206 (t) REVERT: 7 250 ASP cc_start: 0.7263 (m-30) cc_final: 0.6695 (m-30) REVERT: 7 271 GLN cc_start: 0.8880 (pt0) cc_final: 0.8291 (tt0) REVERT: 7 356 LEU cc_start: 0.8859 (mt) cc_final: 0.8527 (mt) REVERT: 7 482 TYR cc_start: 0.8180 (t80) cc_final: 0.7889 (t80) REVERT: 7 528 LYS cc_start: 0.8251 (mptt) cc_final: 0.7771 (mmtp) REVERT: 7 550 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8326 (mttp) REVERT: 7 582 ASP cc_start: 0.7761 (t0) cc_final: 0.7553 (m-30) REVERT: 7 640 GLU cc_start: 0.8045 (tp30) cc_final: 0.7636 (tp30) outliers start: 12 outliers final: 1 residues processed: 968 average time/residue: 0.1979 time to fit residues: 288.5834 Evaluate side-chains 632 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 630 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 214 ARG Chi-restraints excluded: chain 7 residue 476 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 333 GLN 2 391 GLN 2 779 HIS ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 849 GLN 2 856 GLN 3 330 HIS 3 349 ASN 3 351 ASN 3 374 HIS 3 417 GLN ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 569 HIS ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 ASN ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 253 GLN 4 263 ASN 4 287 ASN 4 318 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 447 ASN 4 465 HIS 4 646 HIS 4 691 ASN 4 757 HIS 5 58 ASN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 HIS 5 334 GLN 5 424 GLN ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 458 HIS ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN 6 583 GLN 6 658 GLN 6 698 ASN 6 833 GLN 7 87 GLN 7 89 GLN 7 144 ASN 7 292 ASN 7 334 HIS 7 538 HIS 7 544 GLN 7 554 ASN 7 622 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.140773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118142 restraints weight = 51830.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120204 restraints weight = 40278.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121023 restraints weight = 28012.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121797 restraints weight = 24106.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121998 restraints weight = 21817.618| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30315 Z= 0.244 Angle : 1.072 17.024 41020 Z= 0.553 Chirality : 0.052 0.337 4770 Planarity : 0.006 0.061 5273 Dihedral : 8.146 66.127 4207 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.74 % Favored : 91.30 % Rotamer: Outliers : 3.36 % Allowed : 12.33 % Favored : 84.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 3.29 % Twisted Proline : 0.67 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.12), residues: 3736 helix: -1.39 (0.13), residues: 1304 sheet: -1.78 (0.19), residues: 562 loop : -2.43 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 388 TYR 0.029 0.002 TYR 3 211 PHE 0.056 0.003 PHE 2 484 TRP 0.024 0.002 TRP 2 589 HIS 0.012 0.002 HIS 4 465 Details of bonding type rmsd covalent geometry : bond 0.00542 (30308) covalent geometry : angle 1.06732 (41010) SS BOND : bond 0.01220 ( 5) SS BOND : angle 6.71966 ( 10) hydrogen bonds : bond 0.05500 ( 1075) hydrogen bonds : angle 6.68718 ( 3114) Misc. bond : bond 0.00155 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 727 time to evaluate : 0.904 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 456 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8687 (mm) REVERT: 2 458 ARG cc_start: 0.7539 (ttp-170) cc_final: 0.7243 (ttp-170) REVERT: 2 608 GLU cc_start: 0.7960 (mp0) cc_final: 0.7683 (mp0) REVERT: 2 622 GLU cc_start: 0.7858 (tp30) cc_final: 0.7537 (tp30) REVERT: 2 694 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7270 (ptp-110) REVERT: 2 766 TYR cc_start: 0.7457 (t80) cc_final: 0.7189 (t80) REVERT: 3 23 ASP cc_start: 0.7807 (t0) cc_final: 0.7592 (t0) REVERT: 3 32 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6642 (pp) REVERT: 3 274 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8587 (tp) REVERT: 3 362 ILE cc_start: 0.8157 (mm) cc_final: 0.7939 (tp) REVERT: 3 365 GLN cc_start: 0.8216 (mt0) cc_final: 0.8003 (mt0) REVERT: 3 392 ASN cc_start: 0.7764 (t0) cc_final: 0.7410 (m-40) REVERT: 3 427 SER cc_start: 0.7653 (t) cc_final: 0.7418 (p) REVERT: 3 683 TYR cc_start: 0.8663 (t80) cc_final: 0.8432 (t80) REVERT: 4 192 THR cc_start: 0.8795 (p) cc_final: 0.8435 (t) REVERT: 4 199 MET cc_start: 0.7855 (mmt) cc_final: 0.6841 (mtp) REVERT: 4 312 LYS cc_start: 0.7672 (tptm) cc_final: 0.6484 (tptt) REVERT: 4 350 ASN cc_start: 0.7601 (m-40) cc_final: 0.7311 (m-40) REVERT: 4 434 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6411 (tm-30) REVERT: 4 714 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: 5 464 LEU cc_start: 0.8596 (tt) cc_final: 0.8362 (mm) REVERT: 5 478 CYS cc_start: 0.8215 (m) cc_final: 0.8012 (m) REVERT: 5 590 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8125 (t0) REVERT: 5 621 LYS cc_start: 0.8412 (tptp) cc_final: 0.8119 (tptp) REVERT: 6 648 ASP cc_start: 0.7937 (p0) cc_final: 0.7686 (p0) REVERT: 6 708 ARG cc_start: 0.7448 (tpp-160) cc_final: 0.7185 (tpt170) REVERT: 7 115 GLU cc_start: 0.7669 (tp30) cc_final: 0.7415 (tp30) REVERT: 7 214 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5191 (tpp-160) REVERT: 7 271 GLN cc_start: 0.8781 (pt0) cc_final: 0.8312 (tt0) REVERT: 7 288 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7154 (tm-30) REVERT: 7 356 LEU cc_start: 0.8517 (mt) cc_final: 0.8266 (mt) REVERT: 7 396 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6622 (p0) REVERT: 7 448 MET cc_start: 0.6797 (mpp) cc_final: 0.6573 (mpp) REVERT: 7 515 LEU cc_start: 0.8349 (tt) cc_final: 0.8138 (tp) REVERT: 7 517 ASP cc_start: 0.7454 (p0) cc_final: 0.7206 (p0) REVERT: 7 520 ILE cc_start: 0.8719 (mp) cc_final: 0.8303 (mp) REVERT: 7 528 LYS cc_start: 0.8184 (mptt) cc_final: 0.7897 (mmtp) REVERT: 7 550 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8392 (mttp) REVERT: 7 557 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8364 (pp) REVERT: 7 592 SER cc_start: 0.9327 (p) cc_final: 0.9099 (p) REVERT: 7 625 GLN cc_start: 0.4744 (mt0) cc_final: 0.4503 (tm-30) outliers start: 110 outliers final: 48 residues processed: 796 average time/residue: 0.1832 time to fit residues: 226.8047 Evaluate side-chains 662 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 606 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 299 ASP Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 335 SER Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 518 LEU Chi-restraints excluded: chain 4 residue 576 GLN Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 602 THR Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 714 GLU Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 6 residue 160 MET Chi-restraints excluded: chain 6 residue 166 LEU Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 185 LEU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 299 GLU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 214 ARG Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 553 ILE Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 585 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 195 optimal weight: 0.8980 chunk 218 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 309 optimal weight: 0.0050 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 299 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 313 ASN 2 809 HIS 4 184 ASN 4 287 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 ASN 5 58 ASN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 494 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 6 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122411 restraints weight = 51712.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124277 restraints weight = 37609.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125387 restraints weight = 25774.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126704 restraints weight = 21760.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127047 restraints weight = 19760.005| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30315 Z= 0.168 Angle : 0.960 17.103 41020 Z= 0.487 Chirality : 0.049 0.326 4770 Planarity : 0.005 0.056 5273 Dihedral : 7.421 64.867 4207 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.16 % Favored : 90.82 % Rotamer: Outliers : 3.63 % Allowed : 14.71 % Favored : 81.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.13), residues: 3736 helix: -0.48 (0.13), residues: 1331 sheet: -1.35 (0.21), residues: 534 loop : -2.18 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 324 TYR 0.038 0.002 TYR 6 621 PHE 0.032 0.002 PHE 2 484 TRP 0.021 0.002 TRP 2 589 HIS 0.008 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00342 (30308) covalent geometry : angle 0.95726 (41010) SS BOND : bond 0.00602 ( 5) SS BOND : angle 4.47906 ( 10) hydrogen bonds : bond 0.04396 ( 1075) hydrogen bonds : angle 5.92170 ( 3114) Misc. bond : bond 0.00204 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 707 time to evaluate : 0.993 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 456 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8663 (mp) REVERT: 2 536 ASP cc_start: 0.8099 (m-30) cc_final: 0.7711 (m-30) REVERT: 2 608 GLU cc_start: 0.7907 (mp0) cc_final: 0.7581 (mm-30) REVERT: 2 610 ASP cc_start: 0.6527 (m-30) cc_final: 0.6282 (m-30) REVERT: 3 18 ASP cc_start: 0.8674 (p0) cc_final: 0.6919 (t0) REVERT: 3 23 ASP cc_start: 0.7766 (t0) cc_final: 0.7533 (t0) REVERT: 3 176 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9019 (tt) REVERT: 3 185 ILE cc_start: 0.9401 (mm) cc_final: 0.8993 (mt) REVERT: 3 274 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8712 (tp) REVERT: 3 350 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7710 (mp) REVERT: 3 392 ASN cc_start: 0.7676 (t0) cc_final: 0.7328 (m-40) REVERT: 4 192 THR cc_start: 0.8787 (p) cc_final: 0.8487 (t) REVERT: 4 199 MET cc_start: 0.7831 (mmt) cc_final: 0.6938 (mtp) REVERT: 4 321 ASP cc_start: 0.7551 (p0) cc_final: 0.7151 (p0) REVERT: 4 342 MET cc_start: 0.7483 (mmt) cc_final: 0.6943 (mmt) REVERT: 4 566 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8882 (pp) REVERT: 4 617 GLU cc_start: 0.7918 (tt0) cc_final: 0.7700 (tt0) REVERT: 4 632 ASP cc_start: 0.7786 (m-30) cc_final: 0.7570 (m-30) REVERT: 4 672 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8807 (tp) REVERT: 4 756 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: 5 264 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8233 (pp) REVERT: 5 464 LEU cc_start: 0.8546 (tt) cc_final: 0.8283 (mm) REVERT: 5 478 CYS cc_start: 0.8189 (m) cc_final: 0.7831 (m) REVERT: 5 504 ILE cc_start: 0.8604 (mp) cc_final: 0.8193 (pt) REVERT: 5 544 THR cc_start: 0.7299 (p) cc_final: 0.7096 (t) REVERT: 5 621 LYS cc_start: 0.8236 (tptp) cc_final: 0.8018 (tppt) REVERT: 5 668 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6889 (tt) REVERT: 6 298 SER cc_start: 0.8906 (m) cc_final: 0.8585 (p) REVERT: 6 375 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7421 (ptt-90) REVERT: 6 384 ASP cc_start: 0.7379 (m-30) cc_final: 0.7085 (m-30) REVERT: 6 426 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7530 (mm) REVERT: 6 648 ASP cc_start: 0.7824 (p0) cc_final: 0.7614 (p0) REVERT: 6 654 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7340 (mm-30) REVERT: 6 711 LEU cc_start: 0.7631 (tp) cc_final: 0.6916 (tt) REVERT: 6 749 GLU cc_start: 0.8148 (pm20) cc_final: 0.7799 (pm20) REVERT: 7 209 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5819 (tp40) REVERT: 7 231 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8254 (mmtm) REVERT: 7 271 GLN cc_start: 0.8749 (pt0) cc_final: 0.8254 (tt0) REVERT: 7 288 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7008 (tm-30) REVERT: 7 426 LEU cc_start: 0.7265 (tt) cc_final: 0.6114 (mm) REVERT: 7 459 MET cc_start: 0.6622 (tpp) cc_final: 0.6306 (mtt) REVERT: 7 506 MET cc_start: 0.7642 (mmt) cc_final: 0.7027 (mmm) outliers start: 119 outliers final: 46 residues processed: 786 average time/residue: 0.1695 time to fit residues: 212.9197 Evaluate side-chains 645 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 588 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 222 THR Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 299 ASP Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 315 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 350 ILE Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 518 LEU Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 756 GLU Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 6 residue 166 LEU Chi-restraints excluded: chain 6 residue 262 VAL Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 324 VAL Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 585 ASN Chi-restraints excluded: chain 7 residue 692 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 237 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 160 optimal weight: 0.0370 chunk 276 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 GLN 3 487 HIS 4 350 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 49 GLN 5 359 GLN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN ** 6 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN 6 362 GLN ** 6 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122521 restraints weight = 51088.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124726 restraints weight = 36535.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125593 restraints weight = 25362.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126024 restraints weight = 20860.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126217 restraints weight = 19288.171| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30315 Z= 0.164 Angle : 0.916 16.747 41020 Z= 0.463 Chirality : 0.048 0.310 4770 Planarity : 0.005 0.054 5273 Dihedral : 7.032 61.092 4201 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.49 % Favored : 90.63 % Rotamer: Outliers : 3.88 % Allowed : 17.19 % Favored : 78.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.13), residues: 3736 helix: -0.13 (0.14), residues: 1334 sheet: -1.28 (0.21), residues: 526 loop : -2.09 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 694 TYR 0.026 0.002 TYR 6 621 PHE 0.038 0.002 PHE 3 421 TRP 0.009 0.001 TRP 2 589 HIS 0.005 0.001 HIS 4 259 Details of bonding type rmsd covalent geometry : bond 0.00344 (30308) covalent geometry : angle 0.91394 (41010) SS BOND : bond 0.00594 ( 5) SS BOND : angle 3.87856 ( 10) hydrogen bonds : bond 0.04098 ( 1075) hydrogen bonds : angle 5.63848 ( 3114) Misc. bond : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 626 time to evaluate : 1.038 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 608 GLU cc_start: 0.7878 (mp0) cc_final: 0.7637 (mm-30) REVERT: 3 18 ASP cc_start: 0.8796 (p0) cc_final: 0.6888 (t0) REVERT: 3 23 ASP cc_start: 0.7924 (t0) cc_final: 0.7661 (t0) REVERT: 3 176 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8971 (tt) REVERT: 3 185 ILE cc_start: 0.9394 (mm) cc_final: 0.9074 (mt) REVERT: 3 274 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8682 (tp) REVERT: 3 350 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7644 (mp) REVERT: 3 392 ASN cc_start: 0.7751 (t0) cc_final: 0.7424 (m-40) REVERT: 3 683 TYR cc_start: 0.8667 (t80) cc_final: 0.8388 (t80) REVERT: 4 183 THR cc_start: 0.8083 (m) cc_final: 0.7537 (m) REVERT: 4 192 THR cc_start: 0.8912 (p) cc_final: 0.8661 (t) REVERT: 4 199 MET cc_start: 0.7730 (mmt) cc_final: 0.6860 (mtp) REVERT: 4 234 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7242 (ptm-80) REVERT: 4 264 TYR cc_start: 0.8633 (m-80) cc_final: 0.8131 (m-80) REVERT: 4 321 ASP cc_start: 0.7660 (p0) cc_final: 0.7364 (p0) REVERT: 4 342 MET cc_start: 0.7429 (mmt) cc_final: 0.6990 (mmt) REVERT: 4 540 ILE cc_start: 0.9191 (mt) cc_final: 0.8984 (mm) REVERT: 4 566 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8798 (pp) REVERT: 4 617 GLU cc_start: 0.7836 (tt0) cc_final: 0.7535 (tt0) REVERT: 4 632 ASP cc_start: 0.7777 (m-30) cc_final: 0.7483 (m-30) REVERT: 4 672 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8853 (tp) REVERT: 4 800 SER cc_start: 0.8143 (m) cc_final: 0.7942 (m) REVERT: 5 264 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8343 (pp) REVERT: 5 464 LEU cc_start: 0.8532 (tt) cc_final: 0.8193 (mm) REVERT: 5 478 CYS cc_start: 0.8298 (m) cc_final: 0.7964 (m) REVERT: 5 504 ILE cc_start: 0.8530 (mp) cc_final: 0.8170 (pt) REVERT: 5 544 THR cc_start: 0.7594 (p) cc_final: 0.7348 (t) REVERT: 5 590 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8254 (t0) REVERT: 5 668 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6832 (tt) REVERT: 6 298 SER cc_start: 0.8928 (m) cc_final: 0.8712 (p) REVERT: 6 299 GLU cc_start: 0.7343 (tt0) cc_final: 0.7142 (tt0) REVERT: 6 363 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7441 (mt-10) REVERT: 6 375 ARG cc_start: 0.7481 (ptp90) cc_final: 0.7155 (ptp90) REVERT: 6 384 ASP cc_start: 0.7350 (m-30) cc_final: 0.7078 (m-30) REVERT: 6 426 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7599 (mm) REVERT: 6 654 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7300 (mm-30) REVERT: 6 657 GLU cc_start: 0.7312 (pp20) cc_final: 0.7103 (pp20) REVERT: 7 231 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8355 (mmtm) REVERT: 7 271 GLN cc_start: 0.8798 (pt0) cc_final: 0.8323 (tt0) REVERT: 7 288 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7253 (tm-30) REVERT: 7 402 MET cc_start: 0.5667 (mtt) cc_final: 0.5443 (mtt) REVERT: 7 430 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: 7 459 MET cc_start: 0.6675 (tpp) cc_final: 0.6374 (mtt) REVERT: 7 506 MET cc_start: 0.7613 (mmt) cc_final: 0.7264 (mmm) REVERT: 7 550 LYS cc_start: 0.8644 (mttm) cc_final: 0.8386 (mttp) REVERT: 7 640 GLU cc_start: 0.7516 (tp30) cc_final: 0.7179 (tp30) outliers start: 128 outliers final: 69 residues processed: 708 average time/residue: 0.1619 time to fit residues: 185.5991 Evaluate side-chains 656 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 577 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 294 HIS Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 286 THR Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 350 ILE Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 4 residue 311 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 518 LEU Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 703 ASP Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 519 VAL Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 6 residue 166 LEU Chi-restraints excluded: chain 6 residue 262 VAL Chi-restraints excluded: chain 6 residue 373 MET Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 560 VAL Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 669 HIS Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 430 LYS Chi-restraints excluded: chain 7 residue 585 ASN Chi-restraints excluded: chain 7 residue 692 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 92 optimal weight: 1.9990 chunk 358 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 365 optimal weight: 0.9980 chunk 332 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 351 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 621 HIS 3 259 GLN 4 263 ASN 4 287 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 ASN ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122233 restraints weight = 51237.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124420 restraints weight = 36567.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125467 restraints weight = 25272.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125819 restraints weight = 21074.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126242 restraints weight = 20114.068| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30315 Z= 0.164 Angle : 0.902 16.931 41020 Z= 0.454 Chirality : 0.047 0.327 4770 Planarity : 0.004 0.059 5273 Dihedral : 6.838 63.531 4201 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.86 % Favored : 90.20 % Rotamer: Outliers : 3.75 % Allowed : 18.83 % Favored : 77.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.13), residues: 3736 helix: 0.06 (0.14), residues: 1334 sheet: -1.02 (0.21), residues: 515 loop : -2.09 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 4 234 TYR 0.026 0.002 TYR 7 360 PHE 0.043 0.002 PHE 3 421 TRP 0.005 0.001 TRP 2 589 HIS 0.005 0.001 HIS 6 735 Details of bonding type rmsd covalent geometry : bond 0.00349 (30308) covalent geometry : angle 0.90050 (41010) SS BOND : bond 0.00578 ( 5) SS BOND : angle 3.53340 ( 10) hydrogen bonds : bond 0.03944 ( 1075) hydrogen bonds : angle 5.46785 ( 3114) Misc. bond : bond 0.00149 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 622 time to evaluate : 0.939 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 346 SER cc_start: 0.5317 (OUTLIER) cc_final: 0.4763 (p) REVERT: 2 536 ASP cc_start: 0.7963 (m-30) cc_final: 0.7619 (m-30) REVERT: 3 18 ASP cc_start: 0.8772 (p0) cc_final: 0.6869 (t0) REVERT: 3 23 ASP cc_start: 0.7856 (t0) cc_final: 0.7560 (t0) REVERT: 3 176 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8948 (tt) REVERT: 3 185 ILE cc_start: 0.9409 (mm) cc_final: 0.9081 (mt) REVERT: 3 274 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8742 (tp) REVERT: 3 392 ASN cc_start: 0.7735 (t0) cc_final: 0.7377 (m-40) REVERT: 3 683 TYR cc_start: 0.8711 (t80) cc_final: 0.8453 (t80) REVERT: 4 192 THR cc_start: 0.8975 (p) cc_final: 0.8735 (t) REVERT: 4 199 MET cc_start: 0.7708 (mmt) cc_final: 0.6803 (mtp) REVERT: 4 232 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: 4 264 TYR cc_start: 0.8688 (m-80) cc_final: 0.8006 (m-80) REVERT: 4 312 LYS cc_start: 0.8020 (tptm) cc_final: 0.7350 (mtmm) REVERT: 4 321 ASP cc_start: 0.7691 (p0) cc_final: 0.7422 (p0) REVERT: 4 495 VAL cc_start: 0.4827 (OUTLIER) cc_final: 0.4600 (m) REVERT: 4 558 TYR cc_start: 0.7117 (m-80) cc_final: 0.6825 (m-80) REVERT: 4 566 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8813 (pp) REVERT: 4 632 ASP cc_start: 0.7712 (m-30) cc_final: 0.7428 (m-30) REVERT: 4 672 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8870 (tp) REVERT: 5 264 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8269 (pp) REVERT: 5 464 LEU cc_start: 0.8603 (tt) cc_final: 0.8214 (mm) REVERT: 5 478 CYS cc_start: 0.8331 (m) cc_final: 0.7973 (m) REVERT: 5 504 ILE cc_start: 0.8490 (mp) cc_final: 0.8114 (pt) REVERT: 5 544 THR cc_start: 0.7649 (p) cc_final: 0.7418 (t) REVERT: 5 590 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8270 (t0) REVERT: 5 668 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6789 (tt) REVERT: 5 683 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8682 (tt) REVERT: 6 139 GLN cc_start: 0.7220 (tp-100) cc_final: 0.7003 (tm-30) REVERT: 6 298 SER cc_start: 0.8929 (m) cc_final: 0.8625 (p) REVERT: 6 375 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7303 (ptp90) REVERT: 6 426 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7592 (mm) REVERT: 6 648 ASP cc_start: 0.7872 (p0) cc_final: 0.7407 (p0) REVERT: 6 654 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7183 (mm-30) REVERT: 6 657 GLU cc_start: 0.7499 (pp20) cc_final: 0.7119 (pp20) REVERT: 6 673 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8079 (m110) REVERT: 6 723 ILE cc_start: 0.7516 (pt) cc_final: 0.7108 (mm) REVERT: 6 736 MET cc_start: 0.6347 (mmm) cc_final: 0.6040 (mmm) REVERT: 6 749 GLU cc_start: 0.8291 (pm20) cc_final: 0.7988 (pm20) REVERT: 7 231 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8375 (mmtm) REVERT: 7 271 GLN cc_start: 0.8839 (pt0) cc_final: 0.8375 (tt0) REVERT: 7 396 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6574 (p0) REVERT: 7 402 MET cc_start: 0.6083 (mtt) cc_final: 0.5753 (mtt) REVERT: 7 459 MET cc_start: 0.6769 (tpp) cc_final: 0.6497 (mtt) REVERT: 7 506 MET cc_start: 0.7629 (mmt) cc_final: 0.7231 (mmm) REVERT: 7 550 LYS cc_start: 0.8593 (mttm) cc_final: 0.8329 (mttp) REVERT: 7 640 GLU cc_start: 0.7505 (tp30) cc_final: 0.7207 (tp30) outliers start: 124 outliers final: 70 residues processed: 703 average time/residue: 0.1680 time to fit residues: 189.7627 Evaluate side-chains 650 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 566 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 PHE Chi-restraints excluded: chain 2 residue 294 HIS Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 2 residue 803 PHE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 335 SER Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 495 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 798 LEU Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 519 VAL Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 560 VAL Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 673 ASN Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 60 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 64 optimal weight: 0.0030 chunk 70 optimal weight: 0.0980 chunk 31 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 780 GLN 4 287 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 447 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 690 ASN 6 833 GLN 7 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124572 restraints weight = 51413.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126571 restraints weight = 37877.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127500 restraints weight = 26139.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128162 restraints weight = 22109.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128292 restraints weight = 20973.193| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30315 Z= 0.158 Angle : 0.896 17.214 41020 Z= 0.450 Chirality : 0.048 0.339 4770 Planarity : 0.004 0.065 5273 Dihedral : 6.674 60.930 4201 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.73 % Favored : 90.31 % Rotamer: Outliers : 3.91 % Allowed : 19.35 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.41 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3736 helix: 0.20 (0.14), residues: 1329 sheet: -1.00 (0.21), residues: 534 loop : -2.02 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 6 186 TYR 0.029 0.002 TYR 6 621 PHE 0.032 0.002 PHE 3 735 TRP 0.015 0.002 TRP 5 343 HIS 0.008 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00335 (30308) covalent geometry : angle 0.89502 (41010) SS BOND : bond 0.00607 ( 5) SS BOND : angle 3.24548 ( 10) hydrogen bonds : bond 0.03821 ( 1075) hydrogen bonds : angle 5.36037 ( 3114) Misc. bond : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 609 time to evaluate : 1.173 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 346 SER cc_start: 0.5275 (OUTLIER) cc_final: 0.4733 (p) REVERT: 2 536 ASP cc_start: 0.7955 (m-30) cc_final: 0.7697 (m-30) REVERT: 3 18 ASP cc_start: 0.8741 (p0) cc_final: 0.6700 (t70) REVERT: 3 23 ASP cc_start: 0.7892 (t0) cc_final: 0.7637 (t0) REVERT: 3 176 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8890 (tt) REVERT: 3 185 ILE cc_start: 0.9404 (mm) cc_final: 0.9109 (mt) REVERT: 3 274 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8699 (tp) REVERT: 3 392 ASN cc_start: 0.7778 (t0) cc_final: 0.7386 (m-40) REVERT: 3 683 TYR cc_start: 0.8803 (t80) cc_final: 0.8573 (t80) REVERT: 4 177 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5100 (pp) REVERT: 4 192 THR cc_start: 0.8981 (p) cc_final: 0.8743 (t) REVERT: 4 199 MET cc_start: 0.7782 (mmt) cc_final: 0.6831 (mtp) REVERT: 4 264 TYR cc_start: 0.8672 (m-80) cc_final: 0.7961 (m-80) REVERT: 4 272 MET cc_start: 0.7714 (mmm) cc_final: 0.7384 (mmm) REVERT: 4 312 LYS cc_start: 0.8070 (tptm) cc_final: 0.7592 (mtmm) REVERT: 4 321 ASP cc_start: 0.7730 (p0) cc_final: 0.7416 (p0) REVERT: 4 495 VAL cc_start: 0.4746 (OUTLIER) cc_final: 0.4531 (m) REVERT: 4 566 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8804 (pt) REVERT: 4 632 ASP cc_start: 0.7730 (m-30) cc_final: 0.7412 (m-30) REVERT: 4 672 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8871 (tp) REVERT: 4 811 MET cc_start: 0.8149 (tmm) cc_final: 0.7928 (ttp) REVERT: 5 264 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8247 (pp) REVERT: 5 464 LEU cc_start: 0.8548 (tt) cc_final: 0.8183 (mm) REVERT: 5 478 CYS cc_start: 0.8274 (m) cc_final: 0.7920 (m) REVERT: 5 504 ILE cc_start: 0.8434 (mp) cc_final: 0.8100 (pt) REVERT: 5 544 THR cc_start: 0.7762 (p) cc_final: 0.7446 (t) REVERT: 5 590 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8234 (t0) REVERT: 5 668 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6862 (tt) REVERT: 5 681 ILE cc_start: 0.8395 (mp) cc_final: 0.8071 (tt) REVERT: 5 683 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8618 (tt) REVERT: 6 133 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5385 (mp0) REVERT: 6 298 SER cc_start: 0.8862 (m) cc_final: 0.8534 (p) REVERT: 6 375 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7271 (ptp90) REVERT: 6 387 GLU cc_start: 0.7536 (tp30) cc_final: 0.7181 (tp30) REVERT: 6 426 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7590 (mm) REVERT: 6 524 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6830 (p-80) REVERT: 6 525 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6783 (mm) REVERT: 6 648 ASP cc_start: 0.7780 (p0) cc_final: 0.7396 (p0) REVERT: 6 657 GLU cc_start: 0.7390 (pp20) cc_final: 0.7127 (pp20) REVERT: 6 673 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7951 (m110) REVERT: 6 676 THR cc_start: 0.9421 (p) cc_final: 0.9207 (p) REVERT: 6 749 GLU cc_start: 0.8271 (pm20) cc_final: 0.8009 (pm20) REVERT: 7 271 GLN cc_start: 0.8812 (pt0) cc_final: 0.8340 (tt0) REVERT: 7 402 MET cc_start: 0.6042 (mtt) cc_final: 0.5700 (mtt) REVERT: 7 459 MET cc_start: 0.6747 (tpp) cc_final: 0.6372 (mtt) REVERT: 7 506 MET cc_start: 0.7589 (mmt) cc_final: 0.7173 (mmm) REVERT: 7 640 GLU cc_start: 0.7475 (tp30) cc_final: 0.7183 (tp30) outliers start: 129 outliers final: 75 residues processed: 687 average time/residue: 0.1696 time to fit residues: 188.0152 Evaluate side-chains 662 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 571 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 PHE Chi-restraints excluded: chain 2 residue 294 HIS Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 556 VAL Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 669 LEU Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 495 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 LEU Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 798 LEU Chi-restraints excluded: chain 4 residue 826 VAL Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 519 VAL Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 560 VAL Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 673 ASN Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 255 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 322 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 581 ASN 6 833 GLN 7 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123189 restraints weight = 51369.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124790 restraints weight = 39152.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126218 restraints weight = 29446.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126286 restraints weight = 24977.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126549 restraints weight = 22832.222| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30315 Z= 0.166 Angle : 0.899 17.209 41020 Z= 0.452 Chirality : 0.047 0.343 4770 Planarity : 0.005 0.060 5273 Dihedral : 6.592 62.688 4201 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.99 % Allowed : 8.73 % Favored : 90.28 % Rotamer: Outliers : 4.06 % Allowed : 20.24 % Favored : 75.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.13), residues: 3736 helix: 0.26 (0.14), residues: 1325 sheet: -1.08 (0.21), residues: 534 loop : -2.02 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 6 186 TYR 0.030 0.002 TYR 6 621 PHE 0.020 0.002 PHE 3 735 TRP 0.010 0.001 TRP 5 343 HIS 0.018 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00357 (30308) covalent geometry : angle 0.89816 (41010) SS BOND : bond 0.00541 ( 5) SS BOND : angle 3.11569 ( 10) hydrogen bonds : bond 0.03792 ( 1075) hydrogen bonds : angle 5.30249 ( 3114) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 600 time to evaluate : 0.850 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 346 SER cc_start: 0.5261 (OUTLIER) cc_final: 0.4601 (p) REVERT: 2 536 ASP cc_start: 0.7986 (m-30) cc_final: 0.7672 (m-30) REVERT: 3 18 ASP cc_start: 0.8731 (p0) cc_final: 0.6879 (t0) REVERT: 3 23 ASP cc_start: 0.7913 (t0) cc_final: 0.7688 (t0) REVERT: 3 176 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8922 (tt) REVERT: 3 185 ILE cc_start: 0.9374 (mm) cc_final: 0.9066 (mt) REVERT: 3 274 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8683 (tp) REVERT: 3 392 ASN cc_start: 0.7841 (t0) cc_final: 0.7448 (m-40) REVERT: 3 546 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7744 (mp) REVERT: 4 177 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5196 (pp) REVERT: 4 192 THR cc_start: 0.8993 (p) cc_final: 0.8780 (t) REVERT: 4 199 MET cc_start: 0.7736 (mmt) cc_final: 0.6709 (mtp) REVERT: 4 232 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: 4 264 TYR cc_start: 0.8742 (m-80) cc_final: 0.7891 (m-80) REVERT: 4 272 MET cc_start: 0.7649 (mmm) cc_final: 0.7381 (mmm) REVERT: 4 312 LYS cc_start: 0.7901 (tptm) cc_final: 0.7279 (mtmm) REVERT: 4 321 ASP cc_start: 0.7768 (p0) cc_final: 0.7507 (p0) REVERT: 4 495 VAL cc_start: 0.4779 (OUTLIER) cc_final: 0.4516 (m) REVERT: 4 566 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8708 (pp) REVERT: 4 632 ASP cc_start: 0.7675 (m-30) cc_final: 0.7381 (m-30) REVERT: 4 727 LEU cc_start: 0.6673 (pt) cc_final: 0.6457 (pt) REVERT: 4 811 MET cc_start: 0.8131 (tmm) cc_final: 0.7824 (ttp) REVERT: 5 264 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8149 (pp) REVERT: 5 464 LEU cc_start: 0.8551 (tt) cc_final: 0.8179 (mm) REVERT: 5 478 CYS cc_start: 0.8212 (m) cc_final: 0.7879 (m) REVERT: 5 504 ILE cc_start: 0.8218 (mp) cc_final: 0.7939 (pt) REVERT: 5 544 THR cc_start: 0.7765 (p) cc_final: 0.7404 (t) REVERT: 5 590 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8246 (t0) REVERT: 5 668 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7540 (tt) REVERT: 5 683 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8685 (tt) REVERT: 6 133 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: 6 298 SER cc_start: 0.9019 (m) cc_final: 0.8667 (p) REVERT: 6 384 ASP cc_start: 0.7136 (m-30) cc_final: 0.6846 (m-30) REVERT: 6 387 GLU cc_start: 0.7509 (tp30) cc_final: 0.7154 (tp30) REVERT: 6 426 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7595 (mm) REVERT: 6 524 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: 6 657 GLU cc_start: 0.7400 (pp20) cc_final: 0.7174 (pp20) REVERT: 6 749 GLU cc_start: 0.8267 (pm20) cc_final: 0.8010 (pm20) REVERT: 7 190 GLU cc_start: 0.1951 (tm-30) cc_final: 0.1633 (tm-30) REVERT: 7 271 GLN cc_start: 0.8949 (pt0) cc_final: 0.8380 (tt0) REVERT: 7 402 MET cc_start: 0.6026 (mtt) cc_final: 0.5646 (mtt) REVERT: 7 459 MET cc_start: 0.6733 (tpp) cc_final: 0.6322 (mtt) REVERT: 7 506 MET cc_start: 0.7557 (mmt) cc_final: 0.7167 (mmm) REVERT: 7 640 GLU cc_start: 0.7488 (tp30) cc_final: 0.7227 (tp30) outliers start: 134 outliers final: 88 residues processed: 685 average time/residue: 0.1654 time to fit residues: 182.5395 Evaluate side-chains 667 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 564 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 PHE Chi-restraints excluded: chain 2 residue 294 HIS Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 405 HIS Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 533 ILE Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 561 ILE Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 335 SER Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 495 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 798 LEU Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 519 VAL Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 560 VAL Chi-restraints excluded: chain 6 residue 658 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 808 GLU Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 84 ASP Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 124 ASN Chi-restraints excluded: chain 7 residue 125 MET Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 597 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 178 optimal weight: 0.1980 chunk 290 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 262 optimal weight: 0.0170 chunk 225 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123474 restraints weight = 51473.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125502 restraints weight = 38308.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126262 restraints weight = 28488.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126992 restraints weight = 23988.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127148 restraints weight = 22220.592| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30315 Z= 0.162 Angle : 0.901 17.256 41020 Z= 0.452 Chirality : 0.047 0.340 4770 Planarity : 0.004 0.061 5273 Dihedral : 6.546 62.869 4201 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.94 % Favored : 90.10 % Rotamer: Outliers : 3.75 % Allowed : 20.85 % Favored : 75.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.41 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.13), residues: 3736 helix: 0.30 (0.14), residues: 1327 sheet: -1.05 (0.22), residues: 537 loop : -2.03 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG 4 315 TYR 0.026 0.002 TYR 6 621 PHE 0.023 0.001 PHE 3 421 TRP 0.009 0.001 TRP 5 343 HIS 0.019 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00350 (30308) covalent geometry : angle 0.89972 (41010) SS BOND : bond 0.00521 ( 5) SS BOND : angle 2.99388 ( 10) hydrogen bonds : bond 0.03718 ( 1075) hydrogen bonds : angle 5.24021 ( 3114) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 590 time to evaluate : 1.108 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 346 SER cc_start: 0.5324 (OUTLIER) cc_final: 0.4716 (p) REVERT: 2 389 THR cc_start: 0.8455 (p) cc_final: 0.8238 (p) REVERT: 2 536 ASP cc_start: 0.7990 (m-30) cc_final: 0.7694 (m-30) REVERT: 2 608 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6867 (tp30) REVERT: 3 18 ASP cc_start: 0.8681 (p0) cc_final: 0.6848 (t0) REVERT: 3 23 ASP cc_start: 0.7954 (t0) cc_final: 0.7668 (t0) REVERT: 3 176 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8927 (tt) REVERT: 3 185 ILE cc_start: 0.9381 (mm) cc_final: 0.9087 (mt) REVERT: 3 274 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8775 (tp) REVERT: 3 306 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9102 (mtp) REVERT: 3 372 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6005 (m-80) REVERT: 3 392 ASN cc_start: 0.7904 (t0) cc_final: 0.7513 (m-40) REVERT: 3 546 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7859 (mp) REVERT: 3 558 ASP cc_start: 0.5636 (t0) cc_final: 0.5236 (t70) REVERT: 4 177 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5158 (pp) REVERT: 4 192 THR cc_start: 0.8995 (p) cc_final: 0.8793 (t) REVERT: 4 199 MET cc_start: 0.7743 (mmt) cc_final: 0.6687 (mtp) REVERT: 4 264 TYR cc_start: 0.8739 (m-80) cc_final: 0.8255 (m-80) REVERT: 4 272 MET cc_start: 0.7642 (mmm) cc_final: 0.7399 (mmm) REVERT: 4 312 LYS cc_start: 0.7905 (tptm) cc_final: 0.7271 (mtmm) REVERT: 4 566 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8798 (pp) REVERT: 4 632 ASP cc_start: 0.7660 (m-30) cc_final: 0.7364 (m-30) REVERT: 4 811 MET cc_start: 0.8111 (tmm) cc_final: 0.7844 (ttp) REVERT: 5 264 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8154 (pp) REVERT: 5 431 LYS cc_start: 0.9095 (tppt) cc_final: 0.8798 (tppt) REVERT: 5 464 LEU cc_start: 0.8520 (tt) cc_final: 0.8168 (mm) REVERT: 5 478 CYS cc_start: 0.8210 (m) cc_final: 0.7860 (m) REVERT: 5 504 ILE cc_start: 0.8186 (mp) cc_final: 0.7897 (pt) REVERT: 5 544 THR cc_start: 0.7868 (p) cc_final: 0.7520 (t) REVERT: 5 590 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8394 (t0) REVERT: 5 668 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (tt) REVERT: 5 681 ILE cc_start: 0.8350 (mp) cc_final: 0.8099 (tt) REVERT: 5 683 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8673 (tt) REVERT: 6 133 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5398 (mp0) REVERT: 6 178 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7467 (mp) REVERT: 6 298 SER cc_start: 0.9048 (m) cc_final: 0.8657 (p) REVERT: 6 373 MET cc_start: 0.8046 (tmm) cc_final: 0.7809 (tmm) REVERT: 6 384 ASP cc_start: 0.7052 (m-30) cc_final: 0.6842 (m-30) REVERT: 6 426 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7592 (mm) REVERT: 6 524 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6965 (p-80) REVERT: 6 749 GLU cc_start: 0.8251 (pm20) cc_final: 0.8049 (pm20) REVERT: 6 826 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7040 (tp30) REVERT: 7 190 GLU cc_start: 0.2277 (tm-30) cc_final: 0.1828 (tm-30) REVERT: 7 271 GLN cc_start: 0.8934 (pt0) cc_final: 0.8334 (tt0) REVERT: 7 402 MET cc_start: 0.5989 (mtt) cc_final: 0.5687 (mtt) REVERT: 7 459 MET cc_start: 0.6785 (tpp) cc_final: 0.6399 (mtt) REVERT: 7 506 MET cc_start: 0.7538 (mmt) cc_final: 0.6817 (mmt) REVERT: 7 640 GLU cc_start: 0.7500 (tp30) cc_final: 0.7236 (tp30) outliers start: 124 outliers final: 88 residues processed: 666 average time/residue: 0.1763 time to fit residues: 190.5025 Evaluate side-chains 674 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 570 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 PHE Chi-restraints excluded: chain 2 residue 294 HIS Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 405 HIS Chi-restraints excluded: chain 2 residue 416 ASP Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 533 ILE Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 372 TYR Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 561 ILE Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 762 ILE Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 140 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 560 VAL Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 808 GLU Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 84 ASP Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 308 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 318 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 6 833 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125172 restraints weight = 51392.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128009 restraints weight = 37954.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128534 restraints weight = 27253.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128800 restraints weight = 23003.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129033 restraints weight = 20699.665| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30315 Z= 0.155 Angle : 0.909 18.490 41020 Z= 0.455 Chirality : 0.047 0.373 4770 Planarity : 0.005 0.110 5273 Dihedral : 6.433 60.296 4201 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.05 % Favored : 90.10 % Rotamer: Outliers : 3.39 % Allowed : 21.52 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.43 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.13), residues: 3736 helix: 0.32 (0.14), residues: 1327 sheet: -0.92 (0.23), residues: 501 loop : -2.02 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG 4 315 TYR 0.028 0.002 TYR 6 621 PHE 0.027 0.001 PHE 6 142 TRP 0.014 0.002 TRP 2 589 HIS 0.008 0.001 HIS 6 735 Details of bonding type rmsd covalent geometry : bond 0.00327 (30308) covalent geometry : angle 0.90811 (41010) SS BOND : bond 0.00493 ( 5) SS BOND : angle 2.83435 ( 10) hydrogen bonds : bond 0.03631 ( 1075) hydrogen bonds : angle 5.20085 ( 3114) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 620 time to evaluate : 1.045 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 247 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7940 (tpp80) REVERT: 2 346 SER cc_start: 0.4664 (OUTLIER) cc_final: 0.4359 (p) REVERT: 2 536 ASP cc_start: 0.7978 (m-30) cc_final: 0.7669 (m-30) REVERT: 2 608 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6959 (tp30) REVERT: 3 18 ASP cc_start: 0.8583 (p0) cc_final: 0.6617 (t70) REVERT: 3 23 ASP cc_start: 0.7928 (t0) cc_final: 0.7538 (t0) REVERT: 3 167 SER cc_start: 0.9324 (m) cc_final: 0.9064 (t) REVERT: 3 176 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8920 (tt) REVERT: 3 185 ILE cc_start: 0.9378 (mm) cc_final: 0.9082 (mt) REVERT: 3 274 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8746 (tp) REVERT: 3 306 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9039 (mtp) REVERT: 3 392 ASN cc_start: 0.7920 (t0) cc_final: 0.7496 (m-40) REVERT: 3 530 HIS cc_start: 0.5920 (m-70) cc_final: 0.5379 (m-70) REVERT: 3 546 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7841 (mp) REVERT: 3 558 ASP cc_start: 0.5574 (t0) cc_final: 0.5207 (t70) REVERT: 4 192 THR cc_start: 0.9031 (p) cc_final: 0.8771 (t) REVERT: 4 199 MET cc_start: 0.7740 (mmt) cc_final: 0.6687 (mtp) REVERT: 4 264 TYR cc_start: 0.8649 (m-80) cc_final: 0.8151 (m-80) REVERT: 4 312 LYS cc_start: 0.7776 (tptm) cc_final: 0.7287 (mtmm) REVERT: 4 504 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: 4 566 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8811 (pp) REVERT: 4 632 ASP cc_start: 0.7661 (m-30) cc_final: 0.7282 (m-30) REVERT: 5 264 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8160 (pp) REVERT: 5 431 LYS cc_start: 0.9091 (tppt) cc_final: 0.8811 (tppt) REVERT: 5 464 LEU cc_start: 0.8494 (tt) cc_final: 0.8186 (mm) REVERT: 5 471 LEU cc_start: 0.8562 (mt) cc_final: 0.8311 (mt) REVERT: 5 478 CYS cc_start: 0.8259 (m) cc_final: 0.8013 (m) REVERT: 5 504 ILE cc_start: 0.8119 (mp) cc_final: 0.7762 (tp) REVERT: 5 668 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7572 (tt) REVERT: 5 681 ILE cc_start: 0.8263 (mp) cc_final: 0.8031 (tt) REVERT: 5 683 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8603 (tt) REVERT: 6 133 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: 6 178 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7489 (mp) REVERT: 6 185 LEU cc_start: 0.7463 (tt) cc_final: 0.6956 (tp) REVERT: 6 298 SER cc_start: 0.8927 (m) cc_final: 0.8659 (p) REVERT: 6 373 MET cc_start: 0.7907 (tmm) cc_final: 0.7661 (tmm) REVERT: 6 387 GLU cc_start: 0.7392 (tp30) cc_final: 0.7190 (tp30) REVERT: 6 426 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7556 (mm) REVERT: 6 524 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.7101 (p-80) REVERT: 6 736 MET cc_start: 0.6689 (mmm) cc_final: 0.6382 (mmm) REVERT: 6 826 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7042 (tp30) REVERT: 7 21 ILE cc_start: 0.8934 (mm) cc_final: 0.8678 (mm) REVERT: 7 190 GLU cc_start: 0.2184 (tm-30) cc_final: 0.1861 (tm-30) REVERT: 7 240 THR cc_start: 0.9390 (m) cc_final: 0.8907 (p) REVERT: 7 271 GLN cc_start: 0.8911 (pt0) cc_final: 0.8316 (tt0) REVERT: 7 459 MET cc_start: 0.6783 (tpp) cc_final: 0.6373 (mtp) REVERT: 7 506 MET cc_start: 0.7535 (mmt) cc_final: 0.6805 (mmt) REVERT: 7 640 GLU cc_start: 0.7483 (tp30) cc_final: 0.7214 (tp30) outliers start: 112 outliers final: 78 residues processed: 683 average time/residue: 0.1732 time to fit residues: 191.0779 Evaluate side-chains 669 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 577 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 405 HIS Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 533 ILE Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 561 ILE Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 GLN Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 67 HIS Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 140 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 808 GLU Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 84 ASP Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 520 ILE Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Chi-restraints excluded: chain 7 residue 592 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 313 ASN ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 372 ASN ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122778 restraints weight = 51239.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124670 restraints weight = 37606.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125788 restraints weight = 25691.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126069 restraints weight = 21136.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126287 restraints weight = 19949.161| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30315 Z= 0.169 Angle : 0.925 17.493 41020 Z= 0.464 Chirality : 0.048 0.340 4770 Planarity : 0.005 0.081 5273 Dihedral : 6.402 61.873 4201 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.40 % Favored : 89.78 % Rotamer: Outliers : 3.21 % Allowed : 22.01 % Favored : 74.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.43 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.13), residues: 3736 helix: 0.30 (0.14), residues: 1322 sheet: -1.01 (0.22), residues: 529 loop : -1.99 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG 4 315 TYR 0.026 0.002 TYR 5 438 PHE 0.024 0.002 PHE 3 421 TRP 0.008 0.001 TRP 5 343 HIS 0.007 0.001 HIS 7 622 Details of bonding type rmsd covalent geometry : bond 0.00370 (30308) covalent geometry : angle 0.92412 (41010) SS BOND : bond 0.00497 ( 5) SS BOND : angle 2.83369 ( 10) hydrogen bonds : bond 0.03697 ( 1075) hydrogen bonds : angle 5.24636 ( 3114) Misc. bond : bond 0.00103 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 587 time to evaluate : 1.024 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping 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: 2 247 ARG cc_start: 0.8407 (mmp80) cc_final: 0.7916 (tpp80) REVERT: 2 346 SER cc_start: 0.4578 (OUTLIER) cc_final: 0.4355 (p) REVERT: 2 536 ASP cc_start: 0.8023 (m-30) cc_final: 0.7688 (m-30) REVERT: 2 608 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6988 (tp30) REVERT: 2 626 GLN cc_start: 0.8521 (pt0) cc_final: 0.8308 (pt0) REVERT: 2 818 GLU cc_start: 0.8131 (pp20) cc_final: 0.7582 (pp20) REVERT: 3 18 ASP cc_start: 0.8673 (p0) cc_final: 0.6712 (t70) REVERT: 3 23 ASP cc_start: 0.7974 (t0) cc_final: 0.7700 (t0) REVERT: 3 120 TYR cc_start: 0.8035 (m-10) cc_final: 0.7744 (m-10) REVERT: 3 167 SER cc_start: 0.9341 (m) cc_final: 0.9086 (t) REVERT: 3 176 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8942 (tt) REVERT: 3 185 ILE cc_start: 0.9399 (mm) cc_final: 0.9096 (mt) REVERT: 3 274 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8785 (tp) REVERT: 3 372 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: 3 392 ASN cc_start: 0.7988 (t0) cc_final: 0.7545 (m-40) REVERT: 3 530 HIS cc_start: 0.5821 (m-70) cc_final: 0.5264 (m-70) REVERT: 3 546 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7913 (mp) REVERT: 3 558 ASP cc_start: 0.5633 (t0) cc_final: 0.5274 (t70) REVERT: 4 199 MET cc_start: 0.7862 (mmt) cc_final: 0.6766 (mtp) REVERT: 4 264 TYR cc_start: 0.8705 (m-80) cc_final: 0.8226 (m-80) REVERT: 4 312 LYS cc_start: 0.7746 (tptm) cc_final: 0.7368 (mtmm) REVERT: 4 504 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: 4 566 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8912 (pp) REVERT: 4 632 ASP cc_start: 0.7708 (m-30) cc_final: 0.7313 (m-30) REVERT: 4 652 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7087 (mp-120) REVERT: 4 811 MET cc_start: 0.8509 (tmm) cc_final: 0.8056 (ttm) REVERT: 5 264 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8133 (pp) REVERT: 5 431 LYS cc_start: 0.9087 (tppt) cc_final: 0.8792 (tppt) REVERT: 5 464 LEU cc_start: 0.8494 (tt) cc_final: 0.8199 (mm) REVERT: 5 471 LEU cc_start: 0.8615 (mt) cc_final: 0.8348 (mt) REVERT: 5 478 CYS cc_start: 0.8356 (m) cc_final: 0.8026 (m) REVERT: 5 504 ILE cc_start: 0.8143 (mp) cc_final: 0.7767 (tp) REVERT: 5 576 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8137 (t-90) REVERT: 5 590 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8372 (t0) REVERT: 5 668 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7540 (tt) REVERT: 5 683 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8495 (tt) REVERT: 6 133 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5275 (mp0) REVERT: 6 178 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7578 (mp) REVERT: 6 185 LEU cc_start: 0.7526 (tt) cc_final: 0.7053 (tp) REVERT: 6 298 SER cc_start: 0.8962 (m) cc_final: 0.8638 (p) REVERT: 6 373 MET cc_start: 0.7941 (tmm) cc_final: 0.7694 (tmm) REVERT: 6 387 GLU cc_start: 0.7395 (tp30) cc_final: 0.7172 (tp30) REVERT: 6 426 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7576 (mm) REVERT: 6 524 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.7099 (p-80) REVERT: 6 711 LEU cc_start: 0.7297 (tp) cc_final: 0.7089 (tp) REVERT: 6 736 MET cc_start: 0.6937 (mmm) cc_final: 0.6709 (mmm) REVERT: 6 826 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7061 (tp30) REVERT: 7 21 ILE cc_start: 0.8949 (mm) cc_final: 0.8702 (mm) REVERT: 7 190 GLU cc_start: 0.2364 (tm-30) cc_final: 0.2007 (tm-30) REVERT: 7 240 THR cc_start: 0.9397 (m) cc_final: 0.8936 (p) REVERT: 7 271 GLN cc_start: 0.8948 (pt0) cc_final: 0.8348 (tt0) REVERT: 7 459 MET cc_start: 0.6804 (tpp) cc_final: 0.6517 (mmm) REVERT: 7 506 MET cc_start: 0.7542 (mmt) cc_final: 0.6835 (mmt) REVERT: 7 640 GLU cc_start: 0.7534 (tp30) cc_final: 0.7276 (tp30) outliers start: 106 outliers final: 79 residues processed: 651 average time/residue: 0.1714 time to fit residues: 179.9619 Evaluate side-chains 671 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 575 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 320 VAL Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 346 SER Chi-restraints excluded: chain 2 residue 424 VAL Chi-restraints excluded: chain 2 residue 449 THR Chi-restraints excluded: chain 2 residue 501 MET Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 533 ILE Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 598 LEU Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 777 LYS Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 274 ILE Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 372 TYR Chi-restraints excluded: chain 3 residue 427 SER Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 561 ILE Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 427 CYS Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 GLN Chi-restraints excluded: chain 4 residue 682 TYR Chi-restraints excluded: chain 4 residue 692 ILE Chi-restraints excluded: chain 4 residue 708 VAL Chi-restraints excluded: chain 4 residue 747 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 5 residue 54 ILE Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 140 ASN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 193 THR Chi-restraints excluded: chain 5 residue 201 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 5 residue 389 VAL Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 547 LEU Chi-restraints excluded: chain 5 residue 560 HIS Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 683 LEU Chi-restraints excluded: chain 6 residue 133 GLU Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 426 ILE Chi-restraints excluded: chain 6 residue 451 LYS Chi-restraints excluded: chain 6 residue 453 SER Chi-restraints excluded: chain 6 residue 524 HIS Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 688 ARG Chi-restraints excluded: chain 6 residue 792 SER Chi-restraints excluded: chain 6 residue 808 GLU Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 84 ASP Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 344 SER Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 520 ILE Chi-restraints excluded: chain 7 residue 564 LEU Chi-restraints excluded: chain 7 residue 585 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 264 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 204 optimal weight: 0.0970 chunk 325 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 363 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 HIS 5 67 HIS ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122323 restraints weight = 51555.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124173 restraints weight = 37516.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125298 restraints weight = 25731.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125499 restraints weight = 21250.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125693 restraints weight = 20616.799| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30315 Z= 0.169 Angle : 0.922 17.980 41020 Z= 0.461 Chirality : 0.048 0.355 4770 Planarity : 0.005 0.074 5273 Dihedral : 6.377 61.196 4201 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.56 % Favored : 89.61 % Rotamer: Outliers : 3.17 % Allowed : 22.47 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.41 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 3736 helix: 0.28 (0.14), residues: 1329 sheet: -1.04 (0.22), residues: 528 loop : -1.98 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG 4 315 TYR 0.025 0.002 TYR 6 621 PHE 0.026 0.002 PHE 6 142 TRP 0.008 0.002 TRP 5 343 HIS 0.006 0.001 HIS 6 735 Details of bonding type rmsd covalent geometry : bond 0.00370 (30308) covalent geometry : angle 0.92158 (41010) SS BOND : bond 0.00477 ( 5) SS BOND : angle 2.76744 ( 10) hydrogen bonds : bond 0.03653 ( 1075) hydrogen bonds : angle 5.22171 ( 3114) Misc. bond : bond 0.00083 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4757.67 seconds wall clock time: 83 minutes 8.36 seconds (4988.36 seconds total)