Starting phenix.real_space_refine on Wed Jun 25 20:13:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3ja8_6338/06_2025/3ja8_6338_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/3ja8_6338/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3ja8_6338/06_2025/3ja8_6338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3ja8_6338/06_2025/3ja8_6338.map" model { file = "/net/cci-nas-00/data/ceres_data/3ja8_6338/06_2025/3ja8_6338_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3ja8_6338/06_2025/3ja8_6338_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.058 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} 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: 18.13, per 1000 atoms: 0.61 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: 7.98 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.35 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: 10.11 Time building geometry restraints manager: 9.30 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 65.240 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.680 ------------------------------------------------------------------------------- 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 : 29.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.005 TRP 2 589 HIS 0.016 0.002 HIS 4 465 PHE 0.037 0.003 PHE 6 454 TYR 0.038 0.003 TYR 3 211 ARG 0.009 0.001 ARG 7 73 Details of bonding type rmsd hydrogen bonds : bond 0.16538 ( 1075) hydrogen bonds : angle 9.82086 ( 3114) SS BOND : bond 0.00529 ( 5) SS BOND : angle 32.16596 ( 10) covalent geometry : bond 0.01354 (30308) covalent geometry : angle 1.57175 (41010) 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 : 3.215 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: 0.7383 (mp) REVERT: 2 698 PHE cc_start: 0.8306 (t80) cc_final: 0.8090 (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: 0.7209 (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: 0.5410 (t0) REVERT: 4 179 ILE cc_start: 0.6981 (tt) cc_final: 0.6744 (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: 0.7283 (m-40) REVERT: 4 434 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6781 (tm-30) REVERT: 4 444 ILE cc_start: 0.9066 (pp) cc_final: 0.8861 (pt) REVERT: 4 506 LEU cc_start: 0.9236 (mt) cc_final: 0.9021 (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: 0.8302 (mtpp) REVERT: 5 464 LEU cc_start: 0.8696 (tt) cc_final: 0.8448 (mm) REVERT: 5 478 CYS cc_start: 0.8511 (m) cc_final: 0.8176 (m) REVERT: 5 487 ASP cc_start: 0.7891 (m-30) cc_final: 0.7551 (t0) REVERT: 5 519 VAL cc_start: 0.9409 (t) cc_final: 0.9173 (p) REVERT: 5 621 LYS cc_start: 0.8923 (tptp) cc_final: 0.8644 (tptp) REVERT: 6 133 GLU cc_start: 0.6537 (mp0) cc_final: 0.6200 (mp0) REVERT: 6 139 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7504 (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: 0.7183 (t0) REVERT: 7 214 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.4806 (tpp-160) REVERT: 7 241 VAL cc_start: 0.8964 (m) cc_final: 0.8214 (t) REVERT: 7 250 ASP cc_start: 0.7263 (m-30) cc_final: 0.6504 (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: 0.8531 (mt) REVERT: 7 482 TYR cc_start: 0.8180 (t80) cc_final: 0.7886 (t80) REVERT: 7 528 LYS cc_start: 0.8251 (mptt) cc_final: 0.7770 (mmtp) REVERT: 7 550 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8331 (mttp) REVERT: 7 640 GLU cc_start: 0.8045 (tp30) cc_final: 0.7638 (tp30) outliers start: 12 outliers final: 1 residues processed: 968 average time/residue: 0.4714 time to fit residues: 681.1706 Evaluate side-chains 633 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 631 time to evaluate : 3.789 ------------------------------------------------------------------------------- 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 317 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 294 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 341 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 2 809 HIS 2 849 GLN 2 856 GLN 3 330 HIS 3 349 ASN 3 351 ASN 3 374 HIS 3 417 GLN 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 4 318 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 465 HIS 4 492 HIS 4 646 HIS 4 691 ASN 4 757 HIS ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 HIS 5 334 GLN 5 359 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 5 632 GLN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN 6 458 HIS ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN 6 690 ASN 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120861 restraints weight = 51135.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123282 restraints weight = 37283.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124006 restraints weight = 25324.549| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30315 Z= 0.205 Angle : 1.046 17.081 41020 Z= 0.538 Chirality : 0.051 0.325 4770 Planarity : 0.006 0.061 5273 Dihedral : 8.004 65.197 4207 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.20 % Favored : 91.86 % Rotamer: Outliers : 3.05 % Allowed : 12.00 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 3.32 % Twisted Proline : 0.67 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.12), residues: 3736 helix: -1.31 (0.13), residues: 1307 sheet: -1.63 (0.19), residues: 572 loop : -2.32 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP 2 589 HIS 0.012 0.001 HIS 4 465 PHE 0.050 0.002 PHE 2 484 TYR 0.025 0.002 TYR 5 281 ARG 0.008 0.001 ARG 5 324 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 1075) hydrogen bonds : angle 6.57556 ( 3114) SS BOND : bond 0.01151 ( 5) SS BOND : angle 6.46538 ( 10) covalent geometry : bond 0.00435 (30308) covalent geometry : angle 1.04143 (41010) Misc. bond : bond 0.00432 ( 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 859 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 759 time to evaluate : 3.462 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: 2 221 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6770 (mm-30) REVERT: 2 224 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6373 (mtm180) REVERT: 2 456 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8750 (mm) REVERT: 2 458 ARG cc_start: 0.7558 (ttp-170) cc_final: 0.7316 (ttp-170) REVERT: 2 608 GLU cc_start: 0.7935 (mp0) cc_final: 0.7612 (mp0) REVERT: 2 622 GLU cc_start: 0.7719 (tp30) cc_final: 0.7408 (tp30) REVERT: 2 694 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7257 (ptp-110) REVERT: 3 32 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6532 (pp) REVERT: 3 274 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8602 (tp) REVERT: 3 362 ILE cc_start: 0.8123 (mm) cc_final: 0.7917 (tp) REVERT: 3 392 ASN cc_start: 0.7587 (t0) cc_final: 0.7212 (m-40) REVERT: 3 427 SER cc_start: 0.7494 (t) cc_final: 0.7225 (p) REVERT: 3 683 TYR cc_start: 0.8584 (t80) cc_final: 0.8356 (t80) REVERT: 4 192 THR cc_start: 0.8757 (p) cc_final: 0.8393 (t) REVERT: 4 199 MET cc_start: 0.7756 (mmt) cc_final: 0.6748 (mtp) REVERT: 4 312 LYS cc_start: 0.7660 (tptm) cc_final: 0.6668 (tptt) REVERT: 4 350 ASN cc_start: 0.7541 (m-40) cc_final: 0.7272 (m-40) REVERT: 4 434 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6515 (tm-30) REVERT: 4 544 LEU cc_start: 0.9270 (mt) cc_final: 0.9041 (mp) REVERT: 4 777 MET cc_start: 0.8020 (mmm) cc_final: 0.7674 (mmm) REVERT: 5 365 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6712 (mmtm) REVERT: 5 464 LEU cc_start: 0.8591 (tt) cc_final: 0.8356 (mm) REVERT: 5 478 CYS cc_start: 0.8201 (m) cc_final: 0.7986 (m) REVERT: 5 504 ILE cc_start: 0.8642 (mp) cc_final: 0.8149 (pt) REVERT: 5 590 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8094 (t0) REVERT: 5 621 LYS cc_start: 0.8385 (tptp) cc_final: 0.8104 (tptp) REVERT: 6 182 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: 6 513 ILE cc_start: 0.8718 (tt) cc_final: 0.8336 (mm) REVERT: 6 517 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8295 (mmmm) REVERT: 6 749 GLU cc_start: 0.8116 (pm20) cc_final: 0.7761 (pm20) REVERT: 7 97 THR cc_start: 0.7635 (m) cc_final: 0.7393 (m) REVERT: 7 115 GLU cc_start: 0.7830 (tp30) cc_final: 0.7609 (tp30) REVERT: 7 271 GLN cc_start: 0.8705 (pt0) cc_final: 0.8241 (tt0) REVERT: 7 288 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7139 (tm-30) REVERT: 7 356 LEU cc_start: 0.8603 (mt) cc_final: 0.8366 (mt) REVERT: 7 448 MET cc_start: 0.6786 (mpp) cc_final: 0.6569 (mpp) REVERT: 7 517 ASP cc_start: 0.7320 (p0) cc_final: 0.7065 (p0) REVERT: 7 520 ILE cc_start: 0.8660 (mp) cc_final: 0.8269 (mp) REVERT: 7 528 LYS cc_start: 0.8094 (mptt) cc_final: 0.7854 (mmtp) REVERT: 7 592 SER cc_start: 0.9298 (p) cc_final: 0.9090 (p) outliers start: 100 outliers final: 45 residues processed: 816 average time/residue: 0.4679 time to fit residues: 600.7397 Evaluate side-chains 663 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 613 time to evaluate : 4.299 ------------------------------------------------------------------------------- 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 520 PHE 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 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 151 HIS 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 546 LEU Chi-restraints excluded: chain 3 residue 733 LEU 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 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 67 HIS Chi-restraints excluded: chain 5 residue 590 ASN Chi-restraints excluded: chain 5 residue 653 LEU Chi-restraints excluded: chain 6 residue 166 LEU Chi-restraints excluded: chain 6 residue 182 GLN Chi-restraints excluded: chain 6 residue 185 LEU Chi-restraints excluded: chain 6 residue 652 ILE Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 27 THR 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 318 LEU Chi-restraints excluded: chain 7 residue 324 VAL 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 581 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 35 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 294 optimal weight: 6.9990 chunk 342 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 313 ASN 3 259 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 6 583 GLN ** 6 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120800 restraints weight = 51529.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122928 restraints weight = 39415.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123758 restraints weight = 28143.417| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3573 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= 0.184 Angle : 0.963 17.115 41020 Z= 0.489 Chirality : 0.049 0.325 4770 Planarity : 0.005 0.055 5273 Dihedral : 7.451 65.105 4203 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.24 % Favored : 90.71 % Rotamer: Outliers : 3.72 % Allowed : 14.56 % Favored : 81.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.35 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3736 helix: -0.51 (0.13), residues: 1321 sheet: -1.37 (0.20), residues: 550 loop : -2.19 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 2 589 HIS 0.007 0.001 HIS 3 151 PHE 0.042 0.002 PHE 2 484 TYR 0.033 0.002 TYR 6 621 ARG 0.008 0.001 ARG 5 324 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 1075) hydrogen bonds : angle 5.99469 ( 3114) SS BOND : bond 0.00709 ( 5) SS BOND : angle 4.77374 ( 10) covalent geometry : bond 0.00395 (30308) covalent geometry : angle 0.95982 (41010) Misc. bond : bond 0.00171 ( 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 779 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 656 time to evaluate : 3.197 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: 2 456 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8647 (mm) REVERT: 2 608 GLU cc_start: 0.8060 (mp0) cc_final: 0.7571 (mm-30) REVERT: 2 610 ASP cc_start: 0.6614 (m-30) cc_final: 0.6174 (m-30) REVERT: 2 622 GLU cc_start: 0.7814 (tp30) cc_final: 0.7581 (tp30) REVERT: 2 818 GLU cc_start: 0.8045 (pp20) cc_final: 0.7833 (pp20) REVERT: 3 18 ASP cc_start: 0.8734 (p0) cc_final: 0.7010 (t0) REVERT: 3 32 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6798 (pp) REVERT: 3 176 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8985 (tt) REVERT: 3 185 ILE cc_start: 0.9402 (mm) cc_final: 0.9029 (mt) REVERT: 3 274 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8638 (tp) REVERT: 3 350 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7703 (mp) REVERT: 3 392 ASN cc_start: 0.7765 (t0) cc_final: 0.7418 (m-40) REVERT: 3 427 SER cc_start: 0.7484 (t) cc_final: 0.7276 (p) REVERT: 3 683 TYR cc_start: 0.8698 (t80) cc_final: 0.8431 (t80) REVERT: 4 192 THR cc_start: 0.8802 (p) cc_final: 0.8508 (t) REVERT: 4 199 MET cc_start: 0.7906 (mmt) cc_final: 0.6937 (mtp) REVERT: 4 321 ASP cc_start: 0.7544 (p0) cc_final: 0.7120 (p0) REVERT: 4 342 MET cc_start: 0.7449 (mmt) cc_final: 0.7218 (mmt) REVERT: 4 566 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8918 (pp) REVERT: 4 756 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: 4 777 MET cc_start: 0.8046 (mmm) cc_final: 0.7671 (mmm) REVERT: 5 264 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8281 (pp) REVERT: 5 464 LEU cc_start: 0.8618 (tt) cc_final: 0.8302 (mm) REVERT: 5 478 CYS cc_start: 0.8194 (m) cc_final: 0.7840 (m) REVERT: 5 504 ILE cc_start: 0.8511 (mp) cc_final: 0.8102 (pt) REVERT: 5 544 THR cc_start: 0.7344 (p) cc_final: 0.7114 (t) REVERT: 5 621 LYS cc_start: 0.8325 (tptp) cc_final: 0.8067 (tppt) REVERT: 5 668 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7477 (tt) REVERT: 6 182 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: 6 375 ARG cc_start: 0.7898 (ptp90) cc_final: 0.7678 (ptt-90) REVERT: 6 426 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7539 (mm) REVERT: 6 638 ILE cc_start: 0.9120 (mp) cc_final: 0.8892 (mt) REVERT: 7 209 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6058 (tp40) REVERT: 7 231 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8266 (mmtm) REVERT: 7 271 GLN cc_start: 0.8777 (pt0) cc_final: 0.8282 (tt0) REVERT: 7 288 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6983 (tm-30) REVERT: 7 356 LEU cc_start: 0.8566 (mt) cc_final: 0.8350 (mt) REVERT: 7 396 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6633 (p0) REVERT: 7 550 LYS cc_start: 0.8678 (mttm) cc_final: 0.8424 (mttp) outliers start: 123 outliers final: 57 residues processed: 740 average time/residue: 0.4146 time to fit residues: 490.4608 Evaluate side-chains 646 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 576 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 424 VAL Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 2 residue 506 TYR Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 520 PHE 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 151 HIS Chi-restraints excluded: chain 3 residue 166 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 350 ILE Chi-restraints excluded: chain 3 residue 715 VAL Chi-restraints excluded: chain 4 residue 320 ASN 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 566 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 585 THR 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 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 326 PRO 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 182 GLN Chi-restraints excluded: chain 6 residue 262 VAL 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 652 ILE Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 70 VAL 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 255 VAL Chi-restraints excluded: chain 7 residue 256 GLU Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 418 ILE Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 553 ILE 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 261 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 345 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 780 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN 4 350 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117799 restraints weight = 51761.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119995 restraints weight = 38716.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120532 restraints weight = 28785.195| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30315 Z= 0.216 Angle : 0.946 16.736 41020 Z= 0.480 Chirality : 0.049 0.317 4770 Planarity : 0.005 0.060 5273 Dihedral : 7.290 63.092 4201 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.97 % Favored : 90.02 % Rotamer: Outliers : 4.09 % Allowed : 17.16 % Favored : 78.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.32 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3736 helix: -0.26 (0.14), residues: 1329 sheet: -1.43 (0.20), residues: 579 loop : -2.17 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 2 589 HIS 0.006 0.001 HIS 5 676 PHE 0.036 0.002 PHE 3 421 TYR 0.027 0.002 TYR 6 621 ARG 0.006 0.001 ARG 4 178 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 1075) hydrogen bonds : angle 5.76187 ( 3114) SS BOND : bond 0.00678 ( 5) SS BOND : angle 4.17660 ( 10) covalent geometry : bond 0.00487 (30308) covalent geometry : angle 0.94366 (41010) Misc. bond : bond 0.00127 ( 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 743 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 609 time to evaluate : 3.189 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: 2 315 SER cc_start: 0.8612 (t) cc_final: 0.8411 (m) REVERT: 2 536 ASP cc_start: 0.8142 (m-30) cc_final: 0.7702 (m-30) REVERT: 2 608 GLU cc_start: 0.7935 (mp0) cc_final: 0.7673 (mm-30) REVERT: 2 622 GLU cc_start: 0.7938 (tp30) cc_final: 0.7584 (tp30) REVERT: 2 818 GLU cc_start: 0.7951 (pp20) cc_final: 0.7350 (pp20) REVERT: 3 32 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6757 (pp) REVERT: 3 176 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9019 (tt) REVERT: 3 185 ILE cc_start: 0.9394 (mm) cc_final: 0.9141 (mt) REVERT: 3 274 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8650 (tp) REVERT: 3 350 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7727 (mp) REVERT: 3 392 ASN cc_start: 0.7762 (t0) cc_final: 0.7346 (m-40) REVERT: 4 192 THR cc_start: 0.8859 (p) cc_final: 0.8598 (t) REVERT: 4 199 MET cc_start: 0.7983 (mmt) cc_final: 0.6960 (mtp) REVERT: 4 321 ASP cc_start: 0.7719 (p0) cc_final: 0.7386 (p0) REVERT: 4 342 MET cc_start: 0.7472 (mmt) cc_final: 0.7204 (mmt) REVERT: 4 566 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8880 (pp) REVERT: 4 672 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8859 (tp) REVERT: 4 756 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: 5 257 LYS cc_start: 0.8577 (tttt) cc_final: 0.8359 (tttt) REVERT: 5 264 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8231 (pp) REVERT: 5 276 MET cc_start: 0.8323 (mmm) cc_final: 0.7946 (mtp) REVERT: 5 464 LEU cc_start: 0.8518 (tt) cc_final: 0.8268 (mm) REVERT: 5 478 CYS cc_start: 0.8179 (m) cc_final: 0.7886 (m) REVERT: 5 544 THR cc_start: 0.7295 (p) cc_final: 0.7078 (t) REVERT: 5 590 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8117 (t0) REVERT: 5 621 LYS cc_start: 0.8297 (tptp) cc_final: 0.8087 (tppt) REVERT: 5 668 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7464 (tt) REVERT: 6 363 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7456 (mt-10) REVERT: 6 384 ASP cc_start: 0.7562 (m-30) cc_final: 0.7147 (m-30) REVERT: 6 426 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7673 (mm) REVERT: 6 638 ILE cc_start: 0.9143 (mp) cc_final: 0.8930 (mt) REVERT: 6 654 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7362 (mm-30) REVERT: 6 657 GLU cc_start: 0.7555 (pp20) cc_final: 0.7298 (pp20) REVERT: 6 659 GLN cc_start: 0.7191 (tp40) cc_final: 0.6752 (mm-40) REVERT: 6 673 ASN cc_start: 0.8334 (m110) cc_final: 0.8097 (m110) REVERT: 6 711 LEU cc_start: 0.7486 (tp) cc_final: 0.7029 (tp) REVERT: 7 240 THR cc_start: 0.9479 (m) cc_final: 0.8964 (p) REVERT: 7 271 GLN cc_start: 0.8852 (pt0) cc_final: 0.8272 (tt0) REVERT: 7 288 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6885 (tm-30) REVERT: 7 291 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: 7 356 LEU cc_start: 0.8685 (mt) cc_final: 0.8423 (mt) REVERT: 7 396 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6564 (p0) REVERT: 7 506 MET cc_start: 0.7529 (mmt) cc_final: 0.6824 (mmm) REVERT: 7 550 LYS cc_start: 0.8627 (mttm) cc_final: 0.8361 (mttp) REVERT: 7 557 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (pp) REVERT: 7 640 GLU cc_start: 0.7472 (tp30) cc_final: 0.7205 (tp30) outliers start: 134 outliers final: 77 residues processed: 690 average time/residue: 0.3984 time to fit residues: 439.4188 Evaluate side-chains 661 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 570 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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 299 ASP Chi-restraints excluded: chain 2 residue 318 VAL 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 515 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 777 LYS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 166 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 350 ILE Chi-restraints excluded: chain 4 residue 235 GLU Chi-restraints excluded: chain 4 residue 320 ASN Chi-restraints excluded: chain 4 residue 335 SER Chi-restraints excluded: chain 4 residue 420 TYR Chi-restraints excluded: chain 4 residue 504 GLN Chi-restraints excluded: chain 4 residue 509 ILE 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 591 THR Chi-restraints excluded: chain 4 residue 602 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 664 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 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 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 370 LEU 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 385 SER 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 27 THR 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 291 GLN Chi-restraints excluded: chain 7 residue 299 PHE Chi-restraints excluded: chain 7 residue 324 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 427 ASP Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 553 ILE Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 564 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.2544 > 50: distance: 43 - 72: 26.836 distance: 48 - 53: 16.526 distance: 49 - 81: 4.890 distance: 53 - 54: 8.891 distance: 54 - 55: 19.588 distance: 54 - 57: 12.700 distance: 55 - 56: 7.783 distance: 55 - 64: 6.117 distance: 56 - 93: 21.324 distance: 57 - 58: 22.358 distance: 58 - 59: 8.283 distance: 58 - 60: 31.080 distance: 59 - 61: 11.857 distance: 60 - 62: 13.893 distance: 61 - 63: 26.948 distance: 62 - 63: 25.209 distance: 64 - 65: 10.353 distance: 65 - 68: 7.142 distance: 66 - 67: 9.253 distance: 66 - 72: 6.447 distance: 67 - 100: 16.044 distance: 68 - 69: 12.502 distance: 69 - 70: 25.970 distance: 69 - 71: 4.464 distance: 72 - 73: 12.798 distance: 73 - 74: 12.024 distance: 73 - 76: 5.554 distance: 74 - 75: 13.112 distance: 74 - 81: 6.890 distance: 75 - 107: 16.917 distance: 76 - 77: 10.693 distance: 77 - 78: 9.528 distance: 78 - 79: 34.037 distance: 79 - 80: 21.342 distance: 81 - 82: 6.476 distance: 82 - 83: 7.380 distance: 82 - 85: 12.227 distance: 83 - 84: 15.905 distance: 83 - 93: 9.975 distance: 84 - 111: 18.658 distance: 85 - 86: 4.580 distance: 86 - 87: 6.422 distance: 86 - 88: 5.479 distance: 87 - 89: 9.200 distance: 88 - 90: 10.082 distance: 89 - 91: 5.718 distance: 90 - 91: 4.439 distance: 91 - 92: 12.090 distance: 93 - 94: 15.421 distance: 94 - 95: 10.229 distance: 94 - 97: 13.115 distance: 95 - 96: 9.830 distance: 95 - 100: 11.906 distance: 96 - 122: 40.126 distance: 97 - 98: 7.228 distance: 97 - 99: 19.424 distance: 100 - 101: 9.525 distance: 101 - 102: 7.443 distance: 101 - 104: 18.784 distance: 102 - 103: 8.928 distance: 102 - 107: 7.439 distance: 104 - 105: 26.792 distance: 104 - 106: 12.689 distance: 107 - 108: 28.903 distance: 108 - 109: 21.135 distance: 109 - 110: 7.491 distance: 109 - 111: 9.490 distance: 111 - 112: 25.163 distance: 112 - 113: 26.936 distance: 112 - 115: 27.358 distance: 113 - 114: 9.712 distance: 113 - 122: 14.637 distance: 115 - 116: 10.800 distance: 116 - 117: 4.473 distance: 116 - 118: 33.025 distance: 117 - 119: 3.151 distance: 118 - 120: 11.085 distance: 119 - 121: 26.879 distance: 120 - 121: 16.363 distance: 122 - 123: 17.797 distance: 123 - 124: 6.515 distance: 123 - 126: 14.429 distance: 124 - 125: 20.340 distance: 124 - 127: 13.253 distance: 127 - 128: 19.466 distance: 127 - 133: 33.983 distance: 128 - 129: 29.220 distance: 128 - 131: 12.621 distance: 129 - 130: 5.324 distance: 129 - 134: 10.668 distance: 131 - 132: 15.061 distance: 132 - 133: 15.946