Starting phenix.real_space_refine on Sun May 3 17:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409.map" model { file = "/net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tj5_8409/05_2026/5tj5_8409_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 9625 2.51 5 N 2600 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14976 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3391 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'CIS': 16, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 542} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 947 Unresolved non-hydrogen angles: 1317 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'UNK:plan-1': 250, 'GLN:plan1': 5, 'TYR:plan': 4, 'ARG:plan': 4, 'GLU:plan': 9, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 7, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 449 Chain: "B" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1266 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 914 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 139} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 823 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 885 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 869 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 145} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 895 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 922 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 866 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 65 Chain: "L" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 411 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 52} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 949 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 48 Chain: "N" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 978 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 270 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'UNK:plan-1': 54} Unresolved non-hydrogen planarities: 54 Chain: "P" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 726 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 150 Chain: "P" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 270 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 43} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 20, 'ASN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "P" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 541 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 1, 'TRANS': 97} Chain breaks: 3 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 41, 'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'ARG:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 158 Time building chain proxies: 3.49, per 1000 atoms: 0.23 Number of scatterers: 14976 At special positions: 0 Unit cell: (119.658, 130.536, 114.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2710 8.00 N 2600 7.00 C 9625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 724.1 milliseconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 96.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 34 removed outlier: 4.030A pdb=" N UNK A 34 " --> pdb=" O UNK A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 96 removed outlier: 4.148A pdb=" N UNK A 78 " --> pdb=" O UNK A 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N UNK A 96 " --> pdb=" O UNK A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 176 removed outlier: 4.271A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N UNK A 131 " --> pdb=" O UNK A 127 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK A 137 " --> pdb=" O UNK A 133 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N UNK A 138 " --> pdb=" O UNK A 134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N UNK A 139 " --> pdb=" O UNK A 135 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK A 140 " --> pdb=" O UNK A 136 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK A 144 " --> pdb=" O UNK A 140 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N UNK A 145 " --> pdb=" O UNK A 141 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N UNK A 146 " --> pdb=" O UNK A 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK A 149 " --> pdb=" O UNK A 145 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N UNK A 156 " --> pdb=" O UNK A 152 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N UNK A 158 " --> pdb=" O UNK A 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK A 159 " --> pdb=" O UNK A 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N UNK A 174 " --> pdb=" O UNK A 170 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK A 176 " --> pdb=" O UNK A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 278 through 295 removed outlier: 4.658A pdb=" N UNK A 283 " --> pdb=" O UNK A 279 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK A 291 " --> pdb=" O UNK A 287 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N UNK A 292 " --> pdb=" O UNK A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 410 through 421 Proline residue: A 416 - end of helix removed outlier: 3.634A pdb=" N ALA A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.224A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 4.094A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.871A pdb=" N MET A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 removed outlier: 3.567A pdb=" N SER A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.884A pdb=" N TYR A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 547 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.524A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 removed outlier: 3.593A pdb=" N MET A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 657 removed outlier: 3.902A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.631A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 711 through 733 removed outlier: 3.607A pdb=" N PHE A 722 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 753 removed outlier: 3.558A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 763 through 792 removed outlier: 3.603A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 removed outlier: 3.915A pdb=" N HIS A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 4.076A pdb=" N ALA A 821 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 removed outlier: 3.852A pdb=" N ASP B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 4.005A pdb=" N LEU B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 91 removed outlier: 3.506A pdb=" N GLY B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 121 removed outlier: 4.285A pdb=" N ILE B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE B 117 " --> pdb=" O TYR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 173 removed outlier: 4.228A pdb=" N TRP B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 removed outlier: 4.208A pdb=" N ILE B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.756A pdb=" N LEU B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 3.918A pdb=" N CYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET D 27 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 84 removed outlier: 3.763A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 130 removed outlier: 4.045A pdb=" N LEU D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 162 removed outlier: 3.729A pdb=" N ILE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 138 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 14 through 37 removed outlier: 3.826A pdb=" N ALA E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 4.641A pdb=" N VAL E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 122 removed outlier: 3.843A pdb=" N GLY E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY E 92 " --> pdb=" O PHE E 88 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.503A pdb=" N MET E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 133 " --> pdb=" O MET E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 154 removed outlier: 3.846A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 13 No H-bonds generated for 'chain 'F' and resid 11 through 13' Processing helix chain 'F' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 Processing helix chain 'F' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE F 89 " --> pdb=" O TYR F 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 44 " --> pdb=" O CYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 54 through 77 removed outlier: 3.664A pdb=" N ILE G 62 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE G 89 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 137 Processing helix chain 'G' and resid 137 through 153 Processing helix chain 'H' and resid 11 through 13 No H-bonds generated for 'chain 'H' and resid 11 through 13' Processing helix chain 'H' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL H 44 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 54 Processing helix chain 'H' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE H 110 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 137 Processing helix chain 'H' and resid 137 through 153 Processing helix chain 'I' and resid 11 through 13 No H-bonds generated for 'chain 'I' and resid 11 through 13' Processing helix chain 'I' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 44 " --> pdb=" O CYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 122 removed outlier: 3.906A pdb=" N ILE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU I 91 " --> pdb=" O GLY I 87 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 110 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 121 " --> pdb=" O ARG I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 137 Processing helix chain 'I' and resid 137 through 153 Processing helix chain 'J' and resid 11 through 13 No H-bonds generated for 'chain 'J' and resid 11 through 13' Processing helix chain 'J' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 44 " --> pdb=" O CYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 54 through 77 removed outlier: 3.664A pdb=" N ILE J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 137 Processing helix chain 'J' and resid 137 through 153 Processing helix chain 'L' and resid 7 through 16 removed outlier: 3.741A pdb=" N PHE L 11 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA L 16 " --> pdb=" O ILE L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 19 No H-bonds generated for 'chain 'L' and resid 17 through 19' Processing helix chain 'L' and resid 29 through 47 removed outlier: 4.214A pdb=" N VAL L 37 " --> pdb=" O TRP L 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA L 42 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 13 No H-bonds generated for 'chain 'M' and resid 11 through 13' Processing helix chain 'M' and resid 14 through 44 removed outlier: 4.274A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL M 44 " --> pdb=" O CYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 54 Processing helix chain 'M' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 67 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE M 110 " --> pdb=" O PHE M 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 137 Processing helix chain 'M' and resid 137 through 153 Processing helix chain 'N' and resid 11 through 13 No H-bonds generated for 'chain 'N' and resid 11 through 13' Processing helix chain 'N' and resid 14 through 44 removed outlier: 4.274A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL N 44 " --> pdb=" O CYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 54 Processing helix chain 'N' and resid 54 through 77 removed outlier: 3.666A pdb=" N ILE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY N 67 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER N 77 " --> pdb=" O LEU N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE N 89 " --> pdb=" O TYR N 85 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN N 90 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU N 91 " --> pdb=" O GLY N 87 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE N 110 " --> pdb=" O PHE N 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN N 121 " --> pdb=" O ARG N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 137 Processing helix chain 'N' and resid 137 through 153 Processing helix chain 'O' and resid 2 through 25 removed outlier: 4.059A pdb=" N UNK O 6 " --> pdb=" O UNK O 2 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N UNK O 7 " --> pdb=" O UNK O 3 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK O 8 " --> pdb=" O UNK O 4 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK O 12 " --> pdb=" O UNK O 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK O 13 " --> pdb=" O UNK O 9 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK O 18 " --> pdb=" O UNK O 14 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N UNK O 19 " --> pdb=" O UNK O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 100 removed outlier: 4.401A pdb=" N UNK O 91 " --> pdb=" O UNK O 87 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N UNK O 92 " --> pdb=" O UNK O 88 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK O 97 " --> pdb=" O UNK O 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N UNK O 100 " --> pdb=" O UNK O 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 22 removed outlier: 3.775A pdb=" N GLY P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.532A pdb=" N ILE P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 49 removed outlier: 3.764A pdb=" N LYS P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 86 removed outlier: 3.880A pdb=" N LYS P 75 " --> pdb=" O TYR P 71 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN P 81 " --> pdb=" O TYR P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 112 removed outlier: 3.752A pdb=" N LYS P 93 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR P 102 " --> pdb=" O ILE P 98 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP P 105 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN P 106 " --> pdb=" O TYR P 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 134 Processing helix chain 'P' and resid 145 through 149 Processing helix chain 'P' and resid 159 through 163 Processing helix chain 'P' and resid 177 through 196 removed outlier: 3.705A pdb=" N ALA P 187 " --> pdb=" O LYS P 183 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE P 192 " --> pdb=" O TYR P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 228 removed outlier: 3.641A pdb=" N UNK P 211 " --> pdb=" O UNK P 207 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N UNK P 218 " --> pdb=" O UNK P 214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK P 220 " --> pdb=" O UNK P 216 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK P 222 " --> pdb=" O UNK P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 242 Processing helix chain 'P' and resid 250 through 257 removed outlier: 3.697A pdb=" N UNK P 254 " --> pdb=" O UNK P 250 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N UNK P 255 " --> pdb=" O UNK P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 300 removed outlier: 3.878A pdb=" N LEU P 291 " --> pdb=" O HIS P 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU P 294 " --> pdb=" O GLN P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 333 removed outlier: 3.840A pdb=" N ALA P 311 " --> pdb=" O SER P 307 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3918 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: 2.53 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3542 1.33 - 1.45: 3287 1.45 - 1.57: 8273 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 15170 Sorted by residual: bond pdb=" C LEU A 530 " pdb=" N PHE A 531 " ideal model delta sigma weight residual 1.334 1.275 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" CB TRP L 48 " pdb=" CG TRP L 48 " ideal model delta sigma weight residual 1.498 1.393 0.105 3.10e-02 1.04e+03 1.15e+01 bond pdb=" CA ILE A 569 " pdb=" CB ILE A 569 " ideal model delta sigma weight residual 1.538 1.506 0.032 9.80e-03 1.04e+04 1.10e+01 bond pdb=" CA PHE I 88 " pdb=" C PHE I 88 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.27e+00 bond pdb=" CA PHE J 88 " pdb=" C PHE J 88 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.34e-02 5.57e+03 9.21e+00 ... (remaining 15165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 20491 4.29 - 8.59: 255 8.59 - 12.88: 47 12.88 - 17.17: 10 17.17 - 21.46: 8 Bond angle restraints: 20811 Sorted by residual: angle pdb=" N GLY A 570 " pdb=" CA GLY A 570 " pdb=" C GLY A 570 " ideal model delta sigma weight residual 112.17 90.71 21.46 1.40e+00 5.10e-01 2.35e+02 angle pdb=" C UNK A 36 " pdb=" N UNK A 37 " pdb=" CA UNK A 37 " ideal model delta sigma weight residual 121.70 137.58 -15.88 1.80e+00 3.09e-01 7.78e+01 angle pdb=" N PHE F 88 " pdb=" CA PHE F 88 " pdb=" C PHE F 88 " ideal model delta sigma weight residual 110.80 92.89 17.91 2.13e+00 2.20e-01 7.07e+01 angle pdb=" N PHE G 88 " pdb=" CA PHE G 88 " pdb=" C PHE G 88 " ideal model delta sigma weight residual 110.80 92.91 17.89 2.13e+00 2.20e-01 7.06e+01 angle pdb=" N PHE N 88 " pdb=" CA PHE N 88 " pdb=" C PHE N 88 " ideal model delta sigma weight residual 110.80 92.91 17.89 2.13e+00 2.20e-01 7.06e+01 ... (remaining 20806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 8280 16.61 - 33.23: 179 33.23 - 49.84: 45 49.84 - 66.45: 3 66.45 - 83.07: 2 Dihedral angle restraints: 8509 sinusoidal: 1581 harmonic: 6928 Sorted by residual: dihedral pdb=" CA ILE A 569 " pdb=" C ILE A 569 " pdb=" N GLY A 570 " pdb=" CA GLY A 570 " ideal model delta harmonic sigma weight residual -180.00 -125.71 -54.29 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA GLY H 87 " pdb=" C GLY H 87 " pdb=" N PHE H 88 " pdb=" CA PHE H 88 " ideal model delta harmonic sigma weight residual 180.00 134.76 45.24 0 5.00e+00 4.00e-02 8.19e+01 dihedral pdb=" CA GLY M 87 " pdb=" C GLY M 87 " pdb=" N PHE M 88 " pdb=" CA PHE M 88 " ideal model delta harmonic sigma weight residual 180.00 134.80 45.20 0 5.00e+00 4.00e-02 8.17e+01 ... (remaining 8506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2350 0.077 - 0.153: 254 0.153 - 0.230: 24 0.230 - 0.306: 3 0.306 - 0.383: 4 Chirality restraints: 2635 Sorted by residual: chirality pdb=" CA PRO I 10 " pdb=" N PRO I 10 " pdb=" C PRO I 10 " pdb=" CB PRO I 10 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE B 117 " pdb=" CA ILE B 117 " pdb=" CG1 ILE B 117 " pdb=" CG2 ILE B 117 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA PRO L 58 " pdb=" N PRO L 58 " pdb=" C PRO L 58 " pdb=" CB PRO L 58 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2632 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 88 " -0.025 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE N 88 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE N 88 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE N 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE N 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 88 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE N 88 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS P 126 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO P 127 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO P 127 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 127 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 570 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLY A 570 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 570 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 571 " 0.017 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 256 2.58 - 3.36: 24985 3.36 - 4.13: 33348 4.13 - 4.90: 60341 Nonbonded interactions: 118931 Sorted by model distance: nonbonded pdb=" O ASN B 46 " pdb=" CA GLY B 48 " model vdw 1.040 3.440 nonbonded pdb=" C ASN B 46 " pdb=" CA GLY B 48 " model vdw 1.963 3.670 nonbonded pdb=" O GLY A 408 " pdb=" OG1 THR A 411 " model vdw 2.070 3.040 nonbonded pdb=" O ASN B 46 " pdb=" C GLY B 48 " model vdw 2.072 3.270 nonbonded pdb=" O TYR D 90 " pdb=" N ASN D 94 " model vdw 2.101 3.120 ... (remaining 118926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 11 through 18 or (resid 19 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 52 or (res \ id 53 through 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 62 or (resid 63 through 65 and (name N or name CA or name C or nam \ e O or name CB )) or resid 66 through 68 or (resid 69 through 75 and (name N or \ name CA or name C or name O or name CB )) or resid 76 through 84 or (resid 85 th \ rough 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or \ (resid 88 through 91 and (name N or name CA or name C or name O or name CB )) o \ r resid 92 through 96 or (resid 97 and (name N or name CA or name C or name O or \ name CB )) or (resid 98 through 100 and (name N or name CA or name C or name O \ or name CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or n \ ame C or name O or name CB )) or resid 105 or (resid 106 through 108 and (name N \ or name CA or name C or name O or name CB )) or resid 109 or (resid 110 through \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 or (r \ esid 113 through 114 and (name N or name CA or name C or name O or name CB )) or \ (resid 115 through 117 and (name N or name CA or name C or name O or name CB )) \ or (resid 118 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 144 or (resid 145 through 149 and ( \ name N or name CA or name C or name O or name CB )) or resid 150 or (resid 151 t \ hrough 158 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 37 or resid 50 through \ 62 or (resid 63 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 66 through 68 or (resid 69 through 75 and (name N or name CA or nam \ e C or name O or name CB )) or resid 76 through 84 or (resid 85 through 86 and ( \ name N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 thr \ ough 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 or (resid 99 through 100 and (name N or name CA or name C or name O or \ name CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 105 through 108 and (name N or name CA or \ name C or name O or name CB )) or resid 109 or (resid 110 through 111 and (name \ N or name CA or name C or name O or name CB )) or (resid 112 through 127 and (na \ me N or name CA or name C or name O or name CB )) or (resid 128 through 136 and \ (name N or name CA or name C or name O or name CB )) or resid 137 through 138 or \ (resid 139 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 0 through 144 or (resid 145 through 149 and (name N or name CA or name C or name \ O or name CB )) or resid 150 through 152 or (resid 153 through 158 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 through \ 37 or (resid 50 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 58 or (resid 59 through 60 and (name N or name CA or na \ me C or name O or name CB )) or (resid 61 through 65 and (name N or name CA or n \ ame C or name O or name CB )) or resid 66 through 69 or (resid 70 through 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 85 or \ (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 o \ r (resid 88 through 91 and (name N or name CA or name C or name O or name CB )) \ or resid 92 through 95 or (resid 96 through 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name \ CA or name C or name O or name CB )) or (resid 101 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or (resid 112 through 1 \ 17 and (name N or name CA or name C or name O or name CB )) or (resid 118 throug \ h 127 and (name N or name CA or name C or name O or name CB )) or (resid 128 thr \ ough 136 and (name N or name CA or name C or name O or name CB )) or resid 137 o \ r (resid 138 through 139 and (name N or name CA or name C or name O or name CB ) \ ) or resid 140 through 145 or (resid 146 through 149 and (name N or name CA or n \ ame C or name O or name CB )) or resid 150 through 158)) selection = (chain 'H' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or (resid 50 thro \ ugh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thro \ ugh 58 or (resid 59 through 60 and (name N or name CA or name C or name O or nam \ e CB )) or resid 61 or (resid 62 through 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 67 or (resid 68 through 75 and (name N \ or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 \ and (name N or name CA or name C or name O or name CB )) or (resid 79 through 8 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resid \ 88 through 91 and (name N or name CA or name C or name O or name CB )) or resid \ 92 through 96 or (resid 97 and (name N or name CA or name C or name O or name C \ B )) or (resid 98 through 108 and (name N or name CA or name C or name O or name \ CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or name C o \ r name O or name CB )) or (resid 112 through 117 and (name N or name CA or name \ C or name O or name CB )) or (resid 118 through 127 and (name N or name CA or na \ me C or name O or name CB )) or (resid 128 through 136 and (name N or name CA or \ name C or name O or name CB )) or resid 137 or (resid 138 through 139 and (name \ N or name CA or name C or name O or name CB )) or resid 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB )) or resid 142 through 143 or \ (resid 144 through 149 and (name N or name CA or name C or name O or name CB )) \ or resid 150 through 151 or (resid 152 through 158 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'I' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 33 or (res \ id 34 through 35 and (name N or name CA or name C or name O or name CB )) or res \ id 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or ( \ resid 50 through 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 or (resid 57 through 60 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 61 through 65 and (name N or name CA or name C or name O or \ name CB )) or resid 66 through 68 or (resid 69 through 75 and (name N or name CA \ or name C or name O or name CB )) or resid 76 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 87 through 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or name C o \ r name O or name CB )) or (resid 105 through 114 and (name N or name CA or name \ C or name O or name CB )) or resid 115 or (resid 116 through 117 and (name N or \ name CA or name C or name O or name CB )) or (resid 118 through 127 and (name N \ or name CA or name C or name O or name CB )) or (resid 128 through 136 and (name \ N or name CA or name C or name O or name CB )) or resid 137 or (resid 138 throu \ gh 139 and (name N or name CA or name C or name O or name CB )) or resid 140 or \ (resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 143 or (resid 144 through 149 and (name N or name CA or name C or name \ O or name CB )) or resid 150 or (resid 151 through 158 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'J' and (resid 11 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 33 or (resid 34 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 through \ 37 or (resid 50 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 72 or (resid 73 through 75 and (name N or name CA or na \ me C or name O or name CB )) or resid 76 through 84 or (resid 85 through 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 th \ rough 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) \ or resid 101 or (resid 102 through 104 and (name N or name CA or name C or name \ O or name CB )) or resid 105 or (resid 106 through 108 and (name N or name CA or \ name C or name O or name CB )) or (resid 109 through 114 and (name N or name CA \ or name C or name O or name CB )) or resid 115 or (resid 116 through 117 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 118 through 127 and \ (name N or name CA or name C or name O or name CB )) or (resid 128 through 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 or (resid \ 138 through 139 and (name N or name CA or name C or name O or name CB )) or resi \ d 140 through 144 or (resid 145 through 149 and (name N or name CA or name C or \ name O or name CB )) or resid 150 or (resid 151 through 158 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 33 or (res \ id 34 through 35 and (name N or name CA or name C or name O or name CB )) or res \ id 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or ( \ resid 50 through 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 through 60 and (name N or name CA or name C or \ name O or name CB )) or resid 61 or (resid 62 through 65 and (name N or name CA \ or name C or name O or name CB )) or resid 66 through 67 or (resid 68 through 75 \ and (name N or name CA or name C or name O or name CB )) or resid 76 through 77 \ or (resid 78 and (name N or name CA or name C or name O or name CB )) or (resid \ 79 through 86 and (name N or name CA or name C or name O or name CB )) or resid \ 87 or (resid 88 through 91 and (name N or name CA or name C or name O or name C \ B )) or resid 92 through 96 or (resid 97 and (name N or name CA or name C or nam \ e O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA or \ name C or name O or name CB )) or resid 101 or (resid 102 through 104 and (name \ N or name CA or name C or name O or name CB )) or (resid 105 through 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 or (resid 110 th \ rough 111 and (name N or name CA or name C or name O or name CB )) or resid 112 \ or (resid 113 through 114 and (name N or name CA or name C or name O or name CB \ )) or resid 115 or (resid 116 through 117 and (name N or name CA or name C or na \ me O or name CB )) or (resid 118 through 127 and (name N or name CA or name C or \ name O or name CB )) or (resid 128 through 136 and (name N or name CA or name C \ or name O or name CB )) or resid 137 or (resid 138 through 139 and (name N or n \ ame CA or name C or name O or name CB )) or resid 140 or (resid 141 and (name N \ or name CA or name C or name O or name CB )) or resid 142 through 143 or (resid \ 144 through 149 and (name N or name CA or name C or name O or name CB )) or resi \ d 150 or (resid 151 through 158 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'N' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 16 or (resid 17 through 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 or (resid 24 through 26 and (name N or na \ me CA or name C or name O or name CB )) or resid 27 through 33 or (resid 34 thro \ ugh 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or (resid 50 t \ hrough 55 and (name N or name CA or name C or name O or name CB )) or resid 56 o \ r (resid 57 through 60 and (name N or name CA or name C or name O or name CB )) \ or resid 61 or (resid 62 through 65 and (name N or name CA or name C or name O o \ r name CB )) or resid 66 through 67 or (resid 68 through 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and (na \ me N or name CA or name C or name O or name CB )) or (resid 79 through 86 and (n \ ame N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 thro \ ugh 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thro \ ugh 98 or (resid 99 through 100 and (name N or name CA or name C or name O or na \ me CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or name C \ or name O or name CB )) or resid 105 or (resid 106 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 or (resid \ 113 through 114 and (name N or name CA or name C or name O or name CB )) or resi \ d 115 or (resid 116 through 117 and (name N or name CA or name C or name O or na \ me CB )) or (resid 118 through 127 and (name N or name CA or name C or name O or \ name CB )) or (resid 128 through 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 138 or (resid 139 and (name N or name CA or \ name C or name O or name CB )) or resid 140 or (resid 141 and (name N or name CA \ or name C or name O or name CB )) or resid 142 through 143 or (resid 144 throug \ h 149 and (name N or name CA or name C or name O or name CB )) or resid 150 or ( \ resid 151 through 158 and (name N or name CA or name C or name O or name CB )))) \ } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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 : 0.010 0.109 15170 Z= 0.513 Angle : 1.288 21.463 20811 Z= 0.665 Chirality : 0.054 0.383 2635 Planarity : 0.006 0.072 2712 Dihedral : 9.133 83.067 4075 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.38 % Favored : 85.19 % Rotamer: Outliers : 0.12 % Allowed : 1.22 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.64 % Twisted Proline : 2.04 % Twisted General : 1.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.37 (0.11), residues: 2052 helix: -3.99 (0.07), residues: 1462 sheet: None (None), residues: 0 loop : -4.24 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG L 34 TYR 0.034 0.003 TYR B 143 PHE 0.051 0.003 PHE N 88 TRP 0.026 0.004 TRP B 77 HIS 0.013 0.003 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.01039 (15170) covalent geometry : angle 1.28822 (20811) hydrogen bonds : bond 0.31767 ( 1314) hydrogen bonds : angle 10.71661 ( 3918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 520 time to evaluate : 0.457 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: A 474 TYR cc_start: 0.8416 (t80) cc_final: 0.8036 (t80) REVERT: D 20 PHE cc_start: 0.8082 (t80) cc_final: 0.7854 (t80) REVERT: G 138 VAL cc_start: 0.7827 (m) cc_final: 0.5868 (p) REVERT: G 142 TYR cc_start: 0.7545 (m-80) cc_final: 0.7144 (m-80) REVERT: H 77 SER cc_start: 0.5700 (m) cc_final: 0.5342 (p) REVERT: I 135 PHE cc_start: 0.7532 (t80) cc_final: 0.7220 (t80) REVERT: L 46 LEU cc_start: 0.8343 (mt) cc_final: 0.8111 (mt) REVERT: M 113 ASP cc_start: 0.6559 (t70) cc_final: 0.6321 (t0) REVERT: N 58 ILE cc_start: 0.7754 (tp) cc_final: 0.7447 (tt) REVERT: N 59 MET cc_start: 0.8167 (tpp) cc_final: 0.7856 (mmm) REVERT: N 66 TYR cc_start: 0.7326 (m-10) cc_final: 0.7086 (m-10) REVERT: P 73 SER cc_start: 0.8397 (p) cc_final: 0.8146 (t) outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.0898 time to fit residues: 75.5914 Evaluate side-chains 317 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS A 718 HIS A 743 HIS B 46 ASN E 151 ASN N 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101013 restraints weight = 50191.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103091 restraints weight = 29825.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104500 restraints weight = 19772.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105382 restraints weight = 14287.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106068 restraints weight = 11308.940| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15170 Z= 0.206 Angle : 0.889 11.627 20811 Z= 0.465 Chirality : 0.045 0.292 2635 Planarity : 0.005 0.073 2712 Dihedral : 5.774 56.787 2508 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.85 % Favored : 91.86 % Rotamer: Outliers : 4.89 % Allowed : 19.80 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.64 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2052 helix: -0.74 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : -3.52 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 153 TYR 0.031 0.003 TYR J 142 PHE 0.029 0.002 PHE B 80 TRP 0.026 0.003 TRP A 737 HIS 0.009 0.002 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00406 (15170) covalent geometry : angle 0.88920 (20811) hydrogen bonds : bond 0.06368 ( 1314) hydrogen bonds : angle 5.66712 ( 3918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 431 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 THR cc_start: 0.8590 (m) cc_final: 0.8317 (p) REVERT: A 780 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8004 (mt) REVERT: B 15 PHE cc_start: 0.7573 (m-80) cc_final: 0.7257 (m-80) REVERT: B 109 VAL cc_start: 0.9401 (p) cc_final: 0.9200 (m) REVERT: D 20 PHE cc_start: 0.8514 (t80) cc_final: 0.8172 (t80) REVERT: D 145 GLU cc_start: 0.8761 (tt0) cc_final: 0.8501 (mt-10) REVERT: E 66 TYR cc_start: 0.8580 (m-10) cc_final: 0.8134 (m-80) REVERT: E 131 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9050 (mt) REVERT: F 66 TYR cc_start: 0.9003 (m-10) cc_final: 0.8334 (m-80) REVERT: G 142 TYR cc_start: 0.9104 (m-10) cc_final: 0.8645 (m-80) REVERT: H 59 MET cc_start: 0.8367 (tpt) cc_final: 0.7955 (tpt) REVERT: H 77 SER cc_start: 0.8328 (m) cc_final: 0.7713 (p) REVERT: H 138 VAL cc_start: 0.9293 (p) cc_final: 0.7675 (t) REVERT: H 142 TYR cc_start: 0.9180 (m-10) cc_final: 0.8149 (m-80) REVERT: I 24 THR cc_start: 0.9310 (p) cc_final: 0.9079 (t) REVERT: I 63 ILE cc_start: 0.8872 (pt) cc_final: 0.8568 (mp) REVERT: I 135 PHE cc_start: 0.8532 (t80) cc_final: 0.7660 (t80) REVERT: I 138 VAL cc_start: 0.9291 (m) cc_final: 0.8870 (p) REVERT: J 137 GLU cc_start: 0.8824 (tt0) cc_final: 0.8619 (tt0) REVERT: M 24 THR cc_start: 0.8780 (m) cc_final: 0.8560 (t) REVERT: M 63 ILE cc_start: 0.7613 (pt) cc_final: 0.7293 (mp) REVERT: M 85 TYR cc_start: 0.8532 (t80) cc_final: 0.8292 (t80) REVERT: M 88 PHE cc_start: 0.6911 (m-80) cc_final: 0.6679 (m-80) REVERT: M 133 LEU cc_start: 0.9186 (mt) cc_final: 0.8909 (mt) REVERT: N 54 ILE cc_start: 0.9468 (mm) cc_final: 0.9229 (mt) REVERT: N 58 ILE cc_start: 0.7832 (tp) cc_final: 0.7560 (tt) REVERT: P 30 TYR cc_start: 0.8473 (m-80) cc_final: 0.7020 (m-80) outliers start: 40 outliers final: 14 residues processed: 450 average time/residue: 0.0806 time to fit residues: 60.4853 Evaluate side-chains 365 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 349 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 0.0060 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 HIS M 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.116099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103687 restraints weight = 50780.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105747 restraints weight = 30770.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107155 restraints weight = 20741.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108043 restraints weight = 15155.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108739 restraints weight = 12046.539| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15170 Z= 0.166 Angle : 0.759 10.838 20811 Z= 0.398 Chirality : 0.042 0.244 2635 Planarity : 0.004 0.066 2712 Dihedral : 4.785 41.217 2508 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 5.13 % Allowed : 25.18 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2052 helix: 0.46 (0.12), residues: 1655 sheet: None (None), residues: 0 loop : -3.15 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 34 TYR 0.042 0.002 TYR J 142 PHE 0.049 0.002 PHE B 80 TRP 0.022 0.002 TRP A 777 HIS 0.006 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00334 (15170) covalent geometry : angle 0.75915 (20811) hydrogen bonds : bond 0.04849 ( 1314) hydrogen bonds : angle 4.76545 ( 3918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 397 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8350 (tpt) cc_final: 0.7998 (tpt) REVERT: A 552 TYR cc_start: 0.8043 (t80) cc_final: 0.7779 (t80) REVERT: A 571 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.6586 (p0) REVERT: A 719 THR cc_start: 0.8567 (m) cc_final: 0.8329 (p) REVERT: A 725 ASN cc_start: 0.8135 (t0) cc_final: 0.7913 (t0) REVERT: A 773 LEU cc_start: 0.8969 (tt) cc_final: 0.8715 (mt) REVERT: B 6 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7902 (tptt) REVERT: B 15 PHE cc_start: 0.7695 (m-80) cc_final: 0.7451 (m-80) REVERT: B 109 VAL cc_start: 0.9385 (p) cc_final: 0.9122 (m) REVERT: D 20 PHE cc_start: 0.8481 (t80) cc_final: 0.8224 (t80) REVERT: D 27 MET cc_start: 0.8203 (ptp) cc_final: 0.7954 (ptp) REVERT: D 72 TYR cc_start: 0.8884 (m-80) cc_final: 0.8680 (m-80) REVERT: D 145 GLU cc_start: 0.8794 (tt0) cc_final: 0.8553 (mt-10) REVERT: E 30 TYR cc_start: 0.8143 (t80) cc_final: 0.7897 (t80) REVERT: E 66 TYR cc_start: 0.8441 (m-10) cc_final: 0.8128 (m-10) REVERT: E 70 VAL cc_start: 0.9590 (t) cc_final: 0.9361 (m) REVERT: E 74 VAL cc_start: 0.9149 (m) cc_final: 0.8804 (p) REVERT: E 131 LEU cc_start: 0.9494 (tp) cc_final: 0.9081 (mt) REVERT: E 148 LEU cc_start: 0.9182 (mt) cc_final: 0.8899 (pp) REVERT: F 66 TYR cc_start: 0.9020 (m-10) cc_final: 0.8435 (m-80) REVERT: G 142 TYR cc_start: 0.9142 (m-10) cc_final: 0.8811 (m-80) REVERT: H 76 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: H 77 SER cc_start: 0.8674 (m) cc_final: 0.8301 (t) REVERT: I 135 PHE cc_start: 0.8468 (t80) cc_final: 0.7652 (t80) REVERT: J 137 GLU cc_start: 0.8757 (tt0) cc_final: 0.8191 (tm-30) REVERT: L 45 PHE cc_start: 0.9023 (t80) cc_final: 0.8803 (t80) REVERT: N 35 SER cc_start: 0.9395 (p) cc_final: 0.9093 (t) REVERT: N 141 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8495 (mt) REVERT: P 30 TYR cc_start: 0.8642 (m-80) cc_final: 0.7457 (m-80) REVERT: P 51 TYR cc_start: 0.7636 (t80) cc_final: 0.7286 (t80) REVERT: P 199 GLU cc_start: 0.7643 (pm20) cc_final: 0.7284 (pm20) outliers start: 42 outliers final: 20 residues processed: 413 average time/residue: 0.0815 time to fit residues: 56.3245 Evaluate side-chains 365 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 342 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS B 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103102 restraints weight = 50294.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105155 restraints weight = 30217.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106538 restraints weight = 20342.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107408 restraints weight = 14956.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108103 restraints weight = 11931.617| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15170 Z= 0.162 Angle : 0.720 10.534 20811 Z= 0.377 Chirality : 0.042 0.323 2635 Planarity : 0.004 0.065 2712 Dihedral : 4.467 34.175 2508 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.29 % Favored : 93.42 % Rotamer: Outliers : 5.75 % Allowed : 27.63 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 2052 helix: 0.75 (0.13), residues: 1661 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 34 TYR 0.036 0.002 TYR I 66 PHE 0.043 0.002 PHE B 80 TRP 0.025 0.002 TRP A 777 HIS 0.005 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00330 (15170) covalent geometry : angle 0.71994 (20811) hydrogen bonds : bond 0.04397 ( 1314) hydrogen bonds : angle 4.52257 ( 3918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 375 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 THR cc_start: 0.9495 (p) cc_final: 0.9259 (p) REVERT: A 432 MET cc_start: 0.8038 (tpt) cc_final: 0.7696 (tpt) REVERT: A 571 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 725 ASN cc_start: 0.8123 (t0) cc_final: 0.7892 (t0) REVERT: A 777 TRP cc_start: 0.7904 (t60) cc_final: 0.7608 (t60) REVERT: A 788 MET cc_start: 0.8804 (mmm) cc_final: 0.7995 (mmm) REVERT: B 2 ASN cc_start: 0.8625 (t0) cc_final: 0.8392 (t0) REVERT: B 6 LYS cc_start: 0.8492 (mmmt) cc_final: 0.7980 (tptt) REVERT: B 161 ILE cc_start: 0.7646 (mm) cc_final: 0.7229 (mm) REVERT: D 20 PHE cc_start: 0.8381 (t80) cc_final: 0.8153 (t80) REVERT: D 145 GLU cc_start: 0.8833 (tt0) cc_final: 0.8563 (mt-10) REVERT: E 30 TYR cc_start: 0.8177 (t80) cc_final: 0.7936 (t80) REVERT: E 66 TYR cc_start: 0.8351 (m-10) cc_final: 0.8132 (m-10) REVERT: E 131 LEU cc_start: 0.9485 (tp) cc_final: 0.9054 (mt) REVERT: F 66 TYR cc_start: 0.8964 (m-10) cc_final: 0.8455 (m-80) REVERT: F 89 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8286 (mp) REVERT: G 142 TYR cc_start: 0.8995 (m-10) cc_final: 0.8361 (m-80) REVERT: H 76 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: H 77 SER cc_start: 0.8764 (m) cc_final: 0.8379 (t) REVERT: H 95 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8218 (mm) REVERT: H 138 VAL cc_start: 0.9211 (t) cc_final: 0.7035 (t) REVERT: H 142 TYR cc_start: 0.8475 (m-10) cc_final: 0.8109 (m-80) REVERT: I 24 THR cc_start: 0.9333 (p) cc_final: 0.9099 (t) REVERT: I 63 ILE cc_start: 0.9006 (mp) cc_final: 0.8731 (mp) REVERT: I 135 PHE cc_start: 0.8474 (t80) cc_final: 0.7668 (t80) REVERT: J 88 PHE cc_start: 0.8011 (m-80) cc_final: 0.7810 (m-80) REVERT: J 137 GLU cc_start: 0.8717 (tt0) cc_final: 0.8341 (tt0) REVERT: L 35 SER cc_start: 0.9469 (t) cc_final: 0.9121 (p) REVERT: N 85 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5959 (t80) REVERT: P 30 TYR cc_start: 0.8590 (m-80) cc_final: 0.7496 (m-80) REVERT: P 199 GLU cc_start: 0.7843 (pm20) cc_final: 0.7425 (pm20) outliers start: 47 outliers final: 21 residues processed: 393 average time/residue: 0.0777 time to fit residues: 50.8295 Evaluate side-chains 378 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 49 optimal weight: 0.0270 chunk 94 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 127 optimal weight: 0.0470 chunk 92 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.118805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.106348 restraints weight = 50474.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108306 restraints weight = 31246.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109589 restraints weight = 21451.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110557 restraints weight = 16173.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111151 restraints weight = 12867.336| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15170 Z= 0.146 Angle : 0.704 11.052 20811 Z= 0.363 Chirality : 0.042 0.357 2635 Planarity : 0.003 0.067 2712 Dihedral : 4.195 28.321 2508 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.99 % Favored : 93.71 % Rotamer: Outliers : 5.38 % Allowed : 28.97 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 2052 helix: 0.91 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -3.09 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 34 TYR 0.039 0.001 TYR J 142 PHE 0.034 0.001 PHE B 80 TRP 0.014 0.001 TRP A 777 HIS 0.003 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00287 (15170) covalent geometry : angle 0.70425 (20811) hydrogen bonds : bond 0.04090 ( 1314) hydrogen bonds : angle 4.30029 ( 3918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 776 MET cc_start: 0.7896 (tpt) cc_final: 0.7588 (tpp) REVERT: A 788 MET cc_start: 0.8712 (mmm) cc_final: 0.7949 (mmm) REVERT: B 6 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7791 (tptt) REVERT: B 201 VAL cc_start: 0.9476 (p) cc_final: 0.9249 (p) REVERT: D 20 PHE cc_start: 0.8231 (t80) cc_final: 0.7909 (t80) REVERT: D 141 LEU cc_start: 0.9231 (mt) cc_final: 0.8926 (mt) REVERT: D 145 GLU cc_start: 0.8837 (tt0) cc_final: 0.8542 (mt-10) REVERT: E 30 TYR cc_start: 0.8249 (t80) cc_final: 0.7955 (t80) REVERT: E 131 LEU cc_start: 0.9464 (tp) cc_final: 0.9061 (mt) REVERT: F 66 TYR cc_start: 0.8917 (m-10) cc_final: 0.8460 (m-80) REVERT: G 137 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: G 142 TYR cc_start: 0.9055 (m-10) cc_final: 0.8644 (m-80) REVERT: H 59 MET cc_start: 0.8894 (tpt) cc_final: 0.8415 (tpt) REVERT: H 76 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: H 77 SER cc_start: 0.8757 (m) cc_final: 0.8357 (t) REVERT: H 95 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8140 (mm) REVERT: H 138 VAL cc_start: 0.8982 (t) cc_final: 0.7487 (t) REVERT: H 149 LEU cc_start: 0.8804 (mm) cc_final: 0.8525 (mm) REVERT: I 24 THR cc_start: 0.9325 (p) cc_final: 0.9065 (t) REVERT: I 133 LEU cc_start: 0.9094 (mm) cc_final: 0.8880 (mm) REVERT: I 135 PHE cc_start: 0.8391 (t80) cc_final: 0.7545 (t80) REVERT: J 76 TYR cc_start: 0.8247 (m-80) cc_final: 0.7885 (m-80) REVERT: J 106 PHE cc_start: 0.8336 (t80) cc_final: 0.7973 (t80) REVERT: L 35 SER cc_start: 0.9270 (t) cc_final: 0.8868 (p) REVERT: L 41 LEU cc_start: 0.8749 (tp) cc_final: 0.8508 (tp) REVERT: M 122 GLN cc_start: 0.7471 (tp-100) cc_final: 0.6606 (tm-30) REVERT: N 85 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5904 (t80) REVERT: P 30 TYR cc_start: 0.8606 (m-80) cc_final: 0.7681 (m-80) REVERT: P 199 GLU cc_start: 0.7817 (pm20) cc_final: 0.7360 (pm20) outliers start: 44 outliers final: 20 residues processed: 396 average time/residue: 0.0788 time to fit residues: 52.3256 Evaluate side-chains 375 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 350 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 75 CYS Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 93 optimal weight: 0.1980 chunk 42 optimal weight: 30.0000 chunk 116 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN M 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105970 restraints weight = 50086.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107949 restraints weight = 30925.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109255 restraints weight = 21173.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110220 restraints weight = 15940.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.110913 restraints weight = 12776.059| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15170 Z= 0.149 Angle : 0.710 14.636 20811 Z= 0.364 Chirality : 0.043 0.359 2635 Planarity : 0.003 0.064 2712 Dihedral : 4.082 24.385 2508 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.66 % Rotamer: Outliers : 3.91 % Allowed : 32.40 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 2052 helix: 1.00 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -2.98 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 799 TYR 0.042 0.002 TYR H 142 PHE 0.015 0.001 PHE J 106 TRP 0.026 0.001 TRP A 777 HIS 0.003 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00320 (15170) covalent geometry : angle 0.71019 (20811) hydrogen bonds : bond 0.04042 ( 1314) hydrogen bonds : angle 4.27258 ( 3918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9193 (mt) cc_final: 0.8948 (mm) REVERT: A 733 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7916 (t80) REVERT: A 788 MET cc_start: 0.8639 (mmm) cc_final: 0.7925 (mmm) REVERT: A 806 MET cc_start: 0.8906 (mmm) cc_final: 0.8578 (mmm) REVERT: B 6 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7788 (tptt) REVERT: D 20 PHE cc_start: 0.8058 (t80) cc_final: 0.7838 (t80) REVERT: E 30 TYR cc_start: 0.8303 (t80) cc_final: 0.8001 (t80) REVERT: E 131 LEU cc_start: 0.9330 (tp) cc_final: 0.8979 (mt) REVERT: F 66 TYR cc_start: 0.8836 (m-10) cc_final: 0.8338 (m-80) REVERT: F 89 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8738 (mp) REVERT: F 108 ILE cc_start: 0.9074 (mt) cc_final: 0.8692 (tt) REVERT: G 142 TYR cc_start: 0.8964 (m-10) cc_final: 0.8484 (m-80) REVERT: H 59 MET cc_start: 0.8738 (tpt) cc_final: 0.8236 (tpt) REVERT: H 66 TYR cc_start: 0.8878 (m-80) cc_final: 0.8657 (m-80) REVERT: H 76 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: H 77 SER cc_start: 0.8732 (m) cc_final: 0.8338 (t) REVERT: H 95 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8100 (mm) REVERT: H 142 TYR cc_start: 0.8121 (m-80) cc_final: 0.7611 (m-80) REVERT: H 149 LEU cc_start: 0.8782 (mm) cc_final: 0.8489 (mm) REVERT: I 24 THR cc_start: 0.9322 (p) cc_final: 0.9079 (t) REVERT: I 135 PHE cc_start: 0.8398 (t80) cc_final: 0.7667 (t80) REVERT: J 88 PHE cc_start: 0.7756 (m-80) cc_final: 0.7452 (m-80) REVERT: J 106 PHE cc_start: 0.8361 (t80) cc_final: 0.7986 (t80) REVERT: N 85 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5299 (t80) REVERT: P 30 TYR cc_start: 0.8640 (m-80) cc_final: 0.7716 (m-80) REVERT: P 51 TYR cc_start: 0.7802 (t80) cc_final: 0.7474 (t80) REVERT: P 199 GLU cc_start: 0.7835 (pm20) cc_final: 0.7418 (pm20) outliers start: 32 outliers final: 20 residues processed: 387 average time/residue: 0.0834 time to fit residues: 54.1767 Evaluate side-chains 373 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN I 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103331 restraints weight = 50854.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105255 restraints weight = 31532.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.106581 restraints weight = 21517.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107490 restraints weight = 15976.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108043 restraints weight = 12781.082| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15170 Z= 0.189 Angle : 0.740 11.149 20811 Z= 0.382 Chirality : 0.044 0.371 2635 Planarity : 0.004 0.065 2712 Dihedral : 4.227 23.979 2508 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.38 % Favored : 93.32 % Rotamer: Outliers : 5.87 % Allowed : 34.60 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2052 helix: 0.96 (0.13), residues: 1666 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 34 TYR 0.040 0.002 TYR J 142 PHE 0.036 0.002 PHE N 12 TRP 0.020 0.002 TRP A 777 HIS 0.007 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00406 (15170) covalent geometry : angle 0.73951 (20811) hydrogen bonds : bond 0.04109 ( 1314) hydrogen bonds : angle 4.40969 ( 3918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9246 (mt) cc_final: 0.8981 (mm) REVERT: A 788 MET cc_start: 0.8660 (mmm) cc_final: 0.8023 (mmm) REVERT: B 2 ASN cc_start: 0.8555 (t0) cc_final: 0.8236 (t0) REVERT: B 6 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7733 (tptt) REVERT: D 20 PHE cc_start: 0.8153 (t80) cc_final: 0.7946 (t80) REVERT: D 145 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8142 (mt-10) REVERT: E 30 TYR cc_start: 0.8339 (t80) cc_final: 0.8043 (t80) REVERT: E 131 LEU cc_start: 0.9340 (tp) cc_final: 0.8984 (mt) REVERT: E 148 LEU cc_start: 0.8825 (mt) cc_final: 0.8593 (pp) REVERT: F 66 TYR cc_start: 0.8836 (m-10) cc_final: 0.8356 (m-80) REVERT: F 89 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8612 (mp) REVERT: G 30 TYR cc_start: 0.8428 (t80) cc_final: 0.8002 (t80) REVERT: G 142 TYR cc_start: 0.8948 (m-10) cc_final: 0.8466 (m-80) REVERT: H 59 MET cc_start: 0.8780 (tpt) cc_final: 0.8502 (mmm) REVERT: H 76 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: H 77 SER cc_start: 0.8852 (m) cc_final: 0.8534 (t) REVERT: H 95 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7923 (mm) REVERT: I 24 THR cc_start: 0.9335 (p) cc_final: 0.9116 (t) REVERT: I 135 PHE cc_start: 0.8442 (t80) cc_final: 0.7743 (t80) REVERT: J 150 LEU cc_start: 0.9015 (mm) cc_final: 0.8627 (mm) REVERT: L 43 MET cc_start: 0.8957 (ttm) cc_final: 0.8657 (ttm) REVERT: L 45 PHE cc_start: 0.8980 (t80) cc_final: 0.8705 (t80) REVERT: M 122 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7199 (tm-30) REVERT: N 85 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.5738 (t80) REVERT: N 130 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8734 (tt) REVERT: P 30 TYR cc_start: 0.8591 (m-80) cc_final: 0.7481 (m-80) REVERT: P 199 GLU cc_start: 0.7934 (pm20) cc_final: 0.7509 (pm20) outliers start: 48 outliers final: 30 residues processed: 367 average time/residue: 0.0864 time to fit residues: 53.3363 Evaluate side-chains 368 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 75 CYS Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 90 optimal weight: 4.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 HIS ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106113 restraints weight = 51024.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108105 restraints weight = 31219.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109419 restraints weight = 21254.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110412 restraints weight = 15902.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111104 restraints weight = 12547.396| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15170 Z= 0.147 Angle : 0.730 14.621 20811 Z= 0.367 Chirality : 0.043 0.437 2635 Planarity : 0.003 0.065 2712 Dihedral : 4.062 23.746 2508 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.56 % Favored : 94.20 % Rotamer: Outliers : 4.40 % Allowed : 36.67 % Favored : 58.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 2052 helix: 1.12 (0.13), residues: 1649 sheet: None (None), residues: 0 loop : -2.89 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 799 TYR 0.038 0.002 TYR I 66 PHE 0.023 0.001 PHE J 106 TRP 0.017 0.001 TRP A 777 HIS 0.003 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00310 (15170) covalent geometry : angle 0.72978 (20811) hydrogen bonds : bond 0.03936 ( 1314) hydrogen bonds : angle 4.26953 ( 3918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 367 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 776 MET cc_start: 0.7573 (tpt) cc_final: 0.7280 (tpp) REVERT: A 788 MET cc_start: 0.8725 (mmm) cc_final: 0.8047 (mmm) REVERT: B 6 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7638 (tptt) REVERT: D 20 PHE cc_start: 0.8070 (t80) cc_final: 0.7866 (t80) REVERT: D 72 TYR cc_start: 0.8930 (m-80) cc_final: 0.8346 (t80) REVERT: D 145 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8190 (mt-10) REVERT: E 30 TYR cc_start: 0.8314 (t80) cc_final: 0.8041 (t80) REVERT: E 66 TYR cc_start: 0.8341 (m-10) cc_final: 0.7900 (m-80) REVERT: E 131 LEU cc_start: 0.9327 (tp) cc_final: 0.8974 (mt) REVERT: E 142 TYR cc_start: 0.8891 (m-80) cc_final: 0.8680 (m-80) REVERT: F 66 TYR cc_start: 0.8927 (m-10) cc_final: 0.8379 (m-80) REVERT: F 89 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8656 (mp) REVERT: G 142 TYR cc_start: 0.8950 (m-10) cc_final: 0.8437 (m-80) REVERT: H 76 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7306 (m-10) REVERT: H 77 SER cc_start: 0.8873 (m) cc_final: 0.8567 (t) REVERT: H 95 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8008 (mm) REVERT: H 149 LEU cc_start: 0.8766 (mm) cc_final: 0.8451 (mm) REVERT: I 24 THR cc_start: 0.9339 (p) cc_final: 0.9111 (t) REVERT: I 135 PHE cc_start: 0.8422 (t80) cc_final: 0.7695 (t80) REVERT: J 150 LEU cc_start: 0.8928 (mm) cc_final: 0.8517 (mm) REVERT: L 44 MET cc_start: 0.8576 (mmm) cc_final: 0.8210 (mmm) REVERT: L 47 MET cc_start: 0.8615 (tpp) cc_final: 0.8278 (tpp) REVERT: M 59 MET cc_start: 0.8894 (tpp) cc_final: 0.8664 (tpp) REVERT: M 122 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7054 (tm-30) REVERT: M 137 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8418 (mm-30) REVERT: N 85 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.5610 (t80) REVERT: N 141 LEU cc_start: 0.8817 (mm) cc_final: 0.8483 (mm) REVERT: P 30 TYR cc_start: 0.8579 (m-80) cc_final: 0.7610 (m-80) REVERT: P 199 GLU cc_start: 0.7917 (pm20) cc_final: 0.7578 (pm20) outliers start: 36 outliers final: 24 residues processed: 378 average time/residue: 0.0868 time to fit residues: 54.6454 Evaluate side-chains 376 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 347 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 75 CYS Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 43 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 0.0270 chunk 156 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.119570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107125 restraints weight = 50923.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109136 restraints weight = 31563.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110558 restraints weight = 21509.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111508 restraints weight = 15870.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112103 restraints weight = 12591.407| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15170 Z= 0.144 Angle : 0.737 15.253 20811 Z= 0.369 Chirality : 0.044 0.399 2635 Planarity : 0.003 0.065 2712 Dihedral : 3.961 23.070 2508 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 3.55 % Allowed : 37.53 % Favored : 58.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 2052 helix: 1.09 (0.13), residues: 1662 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 117 TYR 0.039 0.002 TYR J 142 PHE 0.024 0.001 PHE N 12 TRP 0.023 0.002 TRP A 777 HIS 0.003 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00303 (15170) covalent geometry : angle 0.73673 (20811) hydrogen bonds : bond 0.03865 ( 1314) hydrogen bonds : angle 4.25041 ( 3918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 367 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 733 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 788 MET cc_start: 0.8606 (mmm) cc_final: 0.7999 (mmm) REVERT: B 6 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7609 (tptt) REVERT: D 145 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 30 TYR cc_start: 0.8343 (t80) cc_final: 0.8046 (t80) REVERT: E 131 LEU cc_start: 0.9305 (tp) cc_final: 0.8968 (mt) REVERT: E 148 LEU cc_start: 0.8898 (mt) cc_final: 0.8652 (pp) REVERT: F 66 TYR cc_start: 0.8893 (m-10) cc_final: 0.8369 (m-80) REVERT: G 30 TYR cc_start: 0.8368 (t80) cc_final: 0.8160 (t80) REVERT: G 142 TYR cc_start: 0.8894 (m-10) cc_final: 0.8457 (m-80) REVERT: H 76 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: H 77 SER cc_start: 0.8830 (m) cc_final: 0.8537 (t) REVERT: H 95 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7974 (mm) REVERT: H 138 VAL cc_start: 0.9295 (t) cc_final: 0.8327 (t) REVERT: H 142 TYR cc_start: 0.7875 (m-80) cc_final: 0.7242 (m-80) REVERT: H 149 LEU cc_start: 0.8730 (mm) cc_final: 0.8419 (mm) REVERT: I 24 THR cc_start: 0.9340 (p) cc_final: 0.9098 (t) REVERT: I 135 PHE cc_start: 0.8157 (t80) cc_final: 0.7190 (t80) REVERT: J 150 LEU cc_start: 0.8959 (mm) cc_final: 0.8548 (mm) REVERT: L 47 MET cc_start: 0.8611 (tpp) cc_final: 0.8373 (tpp) REVERT: M 59 MET cc_start: 0.8871 (tpp) cc_final: 0.8603 (tpp) REVERT: M 122 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7046 (tm-30) REVERT: M 137 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8525 (mm-30) REVERT: N 85 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.5354 (t80) REVERT: N 141 LEU cc_start: 0.8826 (mm) cc_final: 0.8482 (mm) REVERT: P 30 TYR cc_start: 0.8687 (m-80) cc_final: 0.7667 (m-80) REVERT: P 199 GLU cc_start: 0.7906 (pm20) cc_final: 0.7566 (pm20) outliers start: 29 outliers final: 20 residues processed: 375 average time/residue: 0.0850 time to fit residues: 53.3739 Evaluate side-chains 375 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 75 CYS Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 71 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 78 optimal weight: 0.0870 chunk 79 optimal weight: 0.3980 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.121212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108977 restraints weight = 50585.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110949 restraints weight = 31497.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112352 restraints weight = 21542.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.113198 restraints weight = 15947.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113880 restraints weight = 12841.805| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15170 Z= 0.147 Angle : 0.777 14.442 20811 Z= 0.384 Chirality : 0.045 0.403 2635 Planarity : 0.004 0.065 2712 Dihedral : 3.903 22.812 2508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.97 % Favored : 94.83 % Rotamer: Outliers : 3.42 % Allowed : 39.36 % Favored : 57.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 2052 helix: 1.11 (0.13), residues: 1648 sheet: None (None), residues: 0 loop : -2.75 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 117 TYR 0.039 0.002 TYR J 142 PHE 0.036 0.001 PHE B 121 TRP 0.024 0.002 TRP A 777 HIS 0.004 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00311 (15170) covalent geometry : angle 0.77665 (20811) hydrogen bonds : bond 0.03895 ( 1314) hydrogen bonds : angle 4.28226 ( 3918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 374 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 788 MET cc_start: 0.8598 (mmm) cc_final: 0.7965 (mmm) REVERT: B 1 MET cc_start: 0.6782 (ptp) cc_final: 0.6491 (ptm) REVERT: B 6 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7592 (tptt) REVERT: D 72 TYR cc_start: 0.8728 (m-80) cc_final: 0.7921 (t80) REVERT: D 145 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8412 (mt-10) REVERT: D 149 LEU cc_start: 0.9017 (tt) cc_final: 0.8383 (mm) REVERT: E 30 TYR cc_start: 0.8368 (t80) cc_final: 0.8067 (t80) REVERT: E 131 LEU cc_start: 0.9274 (tp) cc_final: 0.8947 (mt) REVERT: F 66 TYR cc_start: 0.8823 (m-10) cc_final: 0.8459 (m-80) REVERT: G 142 TYR cc_start: 0.8878 (m-10) cc_final: 0.8616 (m-80) REVERT: H 59 MET cc_start: 0.8789 (tpt) cc_final: 0.8559 (tpt) REVERT: H 76 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: H 77 SER cc_start: 0.8805 (m) cc_final: 0.8495 (t) REVERT: H 95 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8043 (mm) REVERT: H 149 LEU cc_start: 0.8732 (mm) cc_final: 0.8418 (mm) REVERT: I 24 THR cc_start: 0.9344 (p) cc_final: 0.9113 (t) REVERT: I 135 PHE cc_start: 0.8112 (t80) cc_final: 0.7139 (t80) REVERT: J 106 PHE cc_start: 0.8340 (t80) cc_final: 0.8055 (t80) REVERT: J 150 LEU cc_start: 0.8950 (mm) cc_final: 0.8496 (mm) REVERT: L 43 MET cc_start: 0.7860 (ttm) cc_final: 0.7643 (ttm) REVERT: L 47 MET cc_start: 0.8598 (tpp) cc_final: 0.8324 (tpp) REVERT: M 59 MET cc_start: 0.8775 (tpp) cc_final: 0.8538 (tpp) REVERT: M 63 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7097 (mp) REVERT: M 122 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7045 (tm-30) REVERT: N 85 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5422 (t80) REVERT: N 90 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: N 141 LEU cc_start: 0.8793 (mm) cc_final: 0.8446 (mm) REVERT: P 51 TYR cc_start: 0.7700 (t80) cc_final: 0.7213 (t80) REVERT: P 199 GLU cc_start: 0.7892 (pm20) cc_final: 0.7562 (pm20) outliers start: 28 outliers final: 15 residues processed: 380 average time/residue: 0.0863 time to fit residues: 54.7412 Evaluate side-chains 377 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 356 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain N residue 75 CYS Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 85 TYR Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN I 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108140 restraints weight = 50349.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110159 restraints weight = 31538.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111566 restraints weight = 21626.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112497 restraints weight = 16002.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113201 restraints weight = 12780.361| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15170 Z= 0.149 Angle : 0.780 17.769 20811 Z= 0.386 Chirality : 0.046 0.458 2635 Planarity : 0.004 0.064 2712 Dihedral : 3.857 22.504 2508 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.36 % Favored : 94.44 % Rotamer: Outliers : 3.18 % Allowed : 41.32 % Favored : 55.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 2052 helix: 1.10 (0.13), residues: 1650 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 117 TYR 0.040 0.002 TYR J 142 PHE 0.046 0.002 PHE B 121 TRP 0.028 0.002 TRP A 777 HIS 0.004 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00321 (15170) covalent geometry : angle 0.78004 (20811) hydrogen bonds : bond 0.03859 ( 1314) hydrogen bonds : angle 4.27928 ( 3918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.29 seconds wall clock time: 40 minutes 37.01 seconds (2437.01 seconds total)