Starting phenix.real_space_refine on Tue Jul 7 03:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpx_32074/07_2026/7vpx_32074.map" } resolution = 3.0 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= 0.000 sd= 0.043 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 316 5.49 5 S 164 5.16 5 C 25154 2.51 5 N 8130 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43240 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 799 Classifications: {'peptide': 147} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 7, 'ARG:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 604 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 14, 'GLN:plan1': 6, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 209 Chain: "J" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 369 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 53} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2754 Inner-chain residues flagged as termini: ['pdbres=" U H 69 "', 'pdbres=" G H 81 "'] Classifications: {'RNA': 130} Modifications used: {'5*END': 2, 'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 55, 'rna3p_pyr': 56} Link IDs: {'rna2p': 19, 'rna3p': 110} Chain breaks: 1 Chain: "1" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "2" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1325 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 45} Link IDs: {'PTRANS': 22, 'TRANS': 164} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "3" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9247 Classifications: {'peptide': 1180} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1119} Chain breaks: 5 Chain: "4" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 664 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 140} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'TYR:plan': 8, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 10, 'ASN:plan1': 9, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 324 Chain: "5" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 504 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 117} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'PHE:plan': 10, 'ASP:plan': 6, 'GLN:plan1': 11, 'ARG:plan': 9, 'ASN:plan1': 4, 'GLU:plan': 14, 'TYR:plan': 5, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 327 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2127 Classifications: {'peptide': 425} Incomplete info: {'backbone_only': 293, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 1490 Unresolved non-hydrogen angles: 2092 Unresolved non-hydrogen dihedrals: 996 Unresolved non-hydrogen chiralities: 366 Planarities with less than four sites: {'GLU:plan': 51, 'GLN:plan1': 17, 'ARG:plan': 25, 'TYR:plan': 18, 'HIS:plan': 7, 'ASP:plan': 22, 'ASN:plan1': 17, 'PHE:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 844 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 2153 Classifications: {'peptide': 455} Incomplete info: {'backbone_only': 345} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 1473 Unresolved non-hydrogen angles: 2114 Unresolved non-hydrogen dihedrals: 915 Unresolved non-hydrogen chiralities: 464 Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 12, 'ARG:plan': 26, 'GLU:plan': 25, 'TRP:plan': 1, 'GLN:plan1': 15, 'HIS:plan': 8, 'TYR:plan': 12, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 648 Chain: "F" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 666 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 150} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 948 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 207 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'ARG:plan': 12, 'ASP:plan': 11, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 305 Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 685 Classifications: {'peptide': 166} Incomplete info: {'backbone_only': 149} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 6, 'ASP:plan': 7, 'GLU:plan': 9, 'PHE:plan': 13, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 337 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 372 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 83} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 10, 'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 308 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASN:plan1': 6, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'TYR:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 319 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "d" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 305 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 5, 'PHE:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 5, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 117 Chain: "e" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 341 Classifications: {'peptide': 83} Incomplete info: {'backbone_only': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 3, 'ARG:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 293 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 130 Chain: "g" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 337 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'HIS:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 314 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "K" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "L" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3485 Classifications: {'RNA': 164} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 13, 'rna3p_pur': 68, 'rna3p_pyr': 72} Link IDs: {'rna2p': 24, 'rna3p': 139} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1643 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 181} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "m" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "h" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "k" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "M" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "l" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "i" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 764 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "j" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' ZN': 3, 'SJT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 135 SG CYS B 56 74.753 111.826 114.577 1.00166.32 S ATOM 158 SG CYS B 59 77.824 111.267 112.284 1.00166.67 S ATOM 24734 SG CYS C 408 91.555 76.678 105.430 1.00 93.55 S ATOM 41567 SG CYS N 6 92.835 166.628 285.244 1.00175.75 S ATOM 41593 SG CYS N 9 90.952 167.499 282.665 1.00127.41 S ATOM 42609 SG CYS 6 11 111.586 102.516 158.498 1.00 81.38 S ATOM 42872 SG CYS 6 46 112.367 102.494 162.268 1.00 86.33 S ATOM 42895 SG CYS 6 49 111.536 105.427 160.989 1.00 98.99 S ATOM 43166 SG CYS 6 85 108.738 102.666 161.110 1.00 76.95 S ATOM 42747 SG CYS 6 30 95.509 102.858 158.687 1.00 93.84 S ATOM 42768 SG CYS 6 33 92.619 102.706 155.487 1.00 90.47 S ATOM 43063 SG CYS 6 72 91.642 100.675 158.242 1.00 84.61 S ATOM 43087 SG CYS 6 75 94.780 99.667 156.533 1.00 80.84 S ATOM 42696 SG CYS 6 23 99.802 115.957 162.644 1.00106.09 S ATOM 42967 SG CYS 6 58 101.920 112.925 162.468 1.00109.30 S ATOM 42988 SG CYS 6 61 101.825 115.579 159.222 1.00114.85 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN 2 624 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN 2 624 " occ=0.00 residue: pdb=" N ALA 2 625 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA 2 625 " occ=0.00 residue: pdb=" N HIS 2 626 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS 2 626 " occ=0.00 residue: pdb=" N LYS 2 627 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS 2 627 " occ=0.00 Time building chain proxies: 8.12, per 1000 atoms: 0.19 Number of scatterers: 43240 At special positions: 0 Unit cell: (168.485, 207.617, 372.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 164 16.00 P 316 15.00 O 9470 8.00 N 8130 7.00 C 25154 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 Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32397 O4' A L 32 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32377 O4' C L 31 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 49 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 85 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 75 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 72 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 58 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 23 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 72 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 56 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 59 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 78 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 425 " pdb="ZN ZN C1000 " - pdb=" ND1 HIS C 431 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 408 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" NE2 HIS N 24 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 30 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 9 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 6 " Number of angles added : 14 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 49 sheets defined 38.0% alpha, 21.0% beta 82 base pairs and 157 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.528A pdb=" N TYR B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.503A pdb=" N GLN B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'D' and resid 47 through 68 Processing helix chain 'D' and resid 97 through 119 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'J' and resid 181 through 215 removed outlier: 3.695A pdb=" N ARG J 206 " --> pdb=" O ALA J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 233 Processing helix chain '1' and resid 491 through 499 removed outlier: 3.615A pdb=" N ARG 1 495 " --> pdb=" O GLU 1 491 " (cutoff:3.500A) Processing helix chain '1' and resid 499 through 506 Processing helix chain '1' and resid 508 through 527 removed outlier: 4.761A pdb=" N ARG 1 524 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU 1 525 " --> pdb=" O ASP 1 521 " (cutoff:3.500A) Processing helix chain '1' and resid 527 through 540 Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 545 through 563 removed outlier: 3.544A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 1 563 " --> pdb=" O ILE 1 559 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 569 No H-bonds generated for 'chain '1' and resid 567 through 569' Processing helix chain '1' and resid 570 through 579 Processing helix chain '1' and resid 586 through 604 Processing helix chain '1' and resid 605 through 614 Processing helix chain '1' and resid 615 through 618 removed outlier: 3.815A pdb=" N ASP 1 618 " --> pdb=" O PRO 1 615 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 615 through 618' Processing helix chain '1' and resid 621 through 640 removed outlier: 3.517A pdb=" N ARG 1 625 " --> pdb=" O ASP 1 621 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN 1 626 " --> pdb=" O GLU 1 622 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR 1 627 " --> pdb=" O TYR 1 623 " (cutoff:3.500A) Processing helix chain '1' and resid 644 through 652 Processing helix chain '1' and resid 657 through 676 removed outlier: 4.010A pdb=" N ARG 1 661 " --> pdb=" O SER 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 677 through 681 removed outlier: 3.875A pdb=" N LEU 1 680 " --> pdb=" O CYS 1 677 " (cutoff:3.500A) Proline residue: 1 681 - end of helix No H-bonds generated for 'chain '1' and resid 677 through 681' Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 692 through 696 removed outlier: 3.758A pdb=" N VAL 1 695 " --> pdb=" O HIS 1 692 " (cutoff:3.500A) Processing helix chain '1' and resid 698 through 717 Processing helix chain '1' and resid 720 through 724 removed outlier: 3.507A pdb=" N SER 1 723 " --> pdb=" O GLY 1 720 " (cutoff:3.500A) Processing helix chain '1' and resid 727 through 738 Processing helix chain '1' and resid 740 through 754 Processing helix chain '1' and resid 755 through 757 No H-bonds generated for 'chain '1' and resid 755 through 757' Processing helix chain '1' and resid 758 through 777 removed outlier: 3.651A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) Processing helix chain '1' and resid 783 through 796 Processing helix chain '1' and resid 802 through 810 Processing helix chain '1' and resid 810 through 818 Processing helix chain '1' and resid 820 through 826 removed outlier: 3.605A pdb=" N ALA 1 824 " --> pdb=" O GLN 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 829 through 845 removed outlier: 3.833A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 845 through 855 removed outlier: 4.204A pdb=" N ILE 1 849 " --> pdb=" O GLY 1 845 " (cutoff:3.500A) Processing helix chain '1' and resid 861 through 880 removed outlier: 3.519A pdb=" N ARG 1 865 " --> pdb=" O ALA 1 861 " (cutoff:3.500A) Processing helix chain '1' and resid 885 through 902 Processing helix chain '1' and resid 907 through 922 removed outlier: 3.892A pdb=" N LEU 1 911 " --> pdb=" O ASP 1 907 " (cutoff:3.500A) Processing helix chain '1' and resid 923 through 925 No H-bonds generated for 'chain '1' and resid 923 through 925' Processing helix chain '1' and resid 927 through 942 removed outlier: 4.430A pdb=" N ASN 1 942 " --> pdb=" O TRP 1 938 " (cutoff:3.500A) Processing helix chain '1' and resid 945 through 964 removed outlier: 3.588A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 981 Processing helix chain '1' and resid 986 through 1002 Processing helix chain '1' and resid 1012 through 1021 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1022 through 1026 removed outlier: 3.534A pdb=" N LYS 11025 " --> pdb=" O PRO 11022 " (cutoff:3.500A) Processing helix chain '1' and resid 1028 through 1046 Processing helix chain '1' and resid 1052 through 1063 removed outlier: 3.604A pdb=" N MET 11056 " --> pdb=" O ALA 11052 " (cutoff:3.500A) Processing helix chain '1' and resid 1064 through 1068 removed outlier: 3.802A pdb=" N LYS 11067 " --> pdb=" O GLU 11064 " (cutoff:3.500A) Processing helix chain '1' and resid 1070 through 1089 Processing helix chain '1' and resid 1089 through 1103 removed outlier: 4.185A pdb=" N VAL 11093 " --> pdb=" O GLY 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1105 through 1123 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1128 through 1136 removed outlier: 3.575A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) Processing helix chain '1' and resid 1143 through 1159 Processing helix chain '1' and resid 1160 through 1164 removed outlier: 3.872A pdb=" N ASP 11164 " --> pdb=" O MET 11161 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1178 removed outlier: 3.696A pdb=" N VAL 11169 " --> pdb=" O TYR 11165 " (cutoff:3.500A) Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1181 through 1199 Processing helix chain '1' and resid 1204 through 1216 removed outlier: 3.604A pdb=" N LEU 11208 " --> pdb=" O CYS 11204 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Processing helix chain '1' and resid 1217 through 1221 removed outlier: 4.211A pdb=" N PHE 11220 " --> pdb=" O PRO 11217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU 11221 " --> pdb=" O ASN 11218 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1217 through 1221' Processing helix chain '1' and resid 1223 through 1241 removed outlier: 3.602A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) Processing helix chain '1' and resid 1242 through 1251 removed outlier: 3.725A pdb=" N MET 11246 " --> pdb=" O GLY 11242 " (cutoff:3.500A) Processing helix chain '1' and resid 1252 through 1254 No H-bonds generated for 'chain '1' and resid 1252 through 1254' Processing helix chain '1' and resid 1258 through 1275 removed outlier: 3.685A pdb=" N GLY 11275 " --> pdb=" O SER 11271 " (cutoff:3.500A) Processing helix chain '1' and resid 1278 through 1283 Processing helix chain '1' and resid 1298 through 1302 Processing helix chain '2' and resid 461 through 469 removed outlier: 3.612A pdb=" N LEU 2 468 " --> pdb=" O GLU 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 475 removed outlier: 3.740A pdb=" N VAL 2 474 " --> pdb=" O ARG 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 482 removed outlier: 4.027A pdb=" N VAL 2 480 " --> pdb=" O MET 2 477 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 2 482 " --> pdb=" O ASP 2 479 " (cutoff:3.500A) Processing helix chain '2' and resid 484 through 493 Processing helix chain '2' and resid 525 through 531 Processing helix chain '2' and resid 567 through 578 removed outlier: 3.593A pdb=" N LEU 2 571 " --> pdb=" O ASP 2 567 " (cutoff:3.500A) Processing helix chain '2' and resid 610 through 618 removed outlier: 3.564A pdb=" N GLY 2 618 " --> pdb=" O ARG 2 614 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 640 removed outlier: 3.714A pdb=" N MET 2 636 " --> pdb=" O TRP 2 632 " (cutoff:3.500A) Processing helix chain '3' and resid 190 through 194 Processing helix chain '3' and resid 429 through 432 removed outlier: 3.522A pdb=" N ARG 3 432 " --> pdb=" O ARG 3 429 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 429 through 432' Processing helix chain '3' and resid 808 through 825 removed outlier: 3.672A pdb=" N GLU 3 825 " --> pdb=" O GLU 3 821 " (cutoff:3.500A) Processing helix chain '3' and resid 838 through 843 Processing helix chain '3' and resid 848 through 853 Processing helix chain '3' and resid 1134 through 1152 removed outlier: 3.576A pdb=" N HIS 31138 " --> pdb=" O SER 31134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1159 through 1164 Processing helix chain '3' and resid 1176 through 1180 Processing helix chain '3' and resid 1181 through 1185 Processing helix chain '3' and resid 1186 through 1195 Processing helix chain '3' and resid 1200 through 1216 removed outlier: 3.642A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR 31215 " --> pdb=" O ILE 31211 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 33 removed outlier: 3.700A pdb=" N TRP 4 30 " --> pdb=" O GLU 4 26 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 74 removed outlier: 3.511A pdb=" N ALA 4 67 " --> pdb=" O SER 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 112 through 121 Processing helix chain '4' and resid 151 through 161 removed outlier: 3.664A pdb=" N SER 4 155 " --> pdb=" O SER 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 46 Processing helix chain '5' and resid 46 through 57 removed outlier: 3.618A pdb=" N LEU 5 50 " --> pdb=" O HIS 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 73 removed outlier: 4.161A pdb=" N LEU 5 73 " --> pdb=" O MET 5 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.897A pdb=" N GLN A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 Processing helix chain 'A' and resid 235 through 272 Processing helix chain 'C' and resid 5 through 28 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.661A pdb=" N ASP C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 4.718A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.556A pdb=" N MET C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.561A pdb=" N VAL C 128 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 181 through 201 removed outlier: 4.000A pdb=" N TYR C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.105A pdb=" N GLY C 224 " --> pdb=" O TRP C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.111A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.533A pdb=" N LYS C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.511A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.516A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.094A pdb=" N LEU C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.624A pdb=" N ALA C 447 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 470 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'E' and resid 153 through 178 Processing helix chain 'E' and resid 226 through 243 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.805A pdb=" N LEU E 355 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.602A pdb=" N GLN E 376 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS E 377 " --> pdb=" O TRP E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 377' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 396 through 408 Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 421 through 437 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 454 through 469 Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.599A pdb=" N GLN E 488 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 530 through 535 Processing helix chain 'E' and resid 539 through 549 Processing helix chain 'E' and resid 564 through 572 Processing helix chain 'E' and resid 603 through 615 removed outlier: 4.196A pdb=" N LEU E 607 " --> pdb=" O GLU E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 642 Processing helix chain 'E' and resid 654 through 668 Processing helix chain 'E' and resid 699 through 709 removed outlier: 3.750A pdb=" N TYR E 703 " --> pdb=" O HIS E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 36 through 40 removed outlier: 4.209A pdb=" N ALA F 39 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 40 " --> pdb=" O LEU F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 40' Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.528A pdb=" N ALA F 86 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.722A pdb=" N ASP F 105 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Proline residue: F 108 - end of helix removed outlier: 3.603A pdb=" N SER F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 61 through 72 removed outlier: 3.510A pdb=" N SER G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 196 through 207 Processing helix chain 'a' and resid 20 through 27 Processing helix chain 'a' and resid 28 through 38 removed outlier: 3.698A pdb=" N LEU a 32 " --> pdb=" O PRO a 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER a 35 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN a 38 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 14 Processing helix chain 'c' and resid 16 through 28 Processing helix chain 'e' and resid 4 through 13 Processing helix chain 'g' and resid 2 through 9 removed outlier: 3.872A pdb=" N PHE g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 80 Processing helix chain 'O' and resid 6 through 11 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 41 through 45 removed outlier: 3.700A pdb=" N ILE O 45 " --> pdb=" O ALA O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 53 Processing helix chain 'O' and resid 63 through 87 removed outlier: 3.580A pdb=" N LYS O 87 " --> pdb=" O GLU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 89 No H-bonds generated for 'chain 'O' and resid 88 through 89' Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 100 through 102 No H-bonds generated for 'chain 'O' and resid 100 through 102' Processing helix chain 'O' and resid 115 through 125 removed outlier: 4.035A pdb=" N VAL O 125 " --> pdb=" O ARG O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 164 Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'h' and resid 3 through 9 removed outlier: 3.612A pdb=" N LEU h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS h 9 " --> pdb=" O ARG h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 80 Processing helix chain 'k' and resid 7 through 11 Processing helix chain 'M' and resid 22 through 36 removed outlier: 4.393A pdb=" N GLN M 36 " --> pdb=" O ALA M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 73 Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'n' and resid 63 through 65 No H-bonds generated for 'chain 'n' and resid 63 through 65' Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'i' and resid 18 through 27 Processing helix chain 'i' and resid 29 through 39 Processing helix chain 'N' and resid 17 through 26 Processing helix chain 'N' and resid 27 through 51 removed outlier: 3.629A pdb=" N GLN N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA N 46 " --> pdb=" O MET N 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU N 49 " --> pdb=" O GLN N 45 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP N 51 " --> pdb=" O GLN N 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 13 Processing helix chain 'j' and resid 74 through 80 Processing helix chain '6' and resid 47 through 55 removed outlier: 7.058A pdb=" N GLY 6 52 " --> pdb=" O CYS 6 49 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER 6 53 " --> pdb=" O ASN 6 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN 6 55 " --> pdb=" O GLY 6 52 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 78 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 121 removed outlier: 4.005A pdb=" N LYS B 118 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 148 through 153 removed outlier: 4.029A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 136 through 141 Processing sheet with id=AA5, first strand: chain '2' and resid 648 through 649 Processing sheet with id=AA6, first strand: chain '3' and resid 1101 through 1108 removed outlier: 3.745A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 31128 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR 3 7 " --> pdb=" O ILE 31128 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 31130 " --> pdb=" O ASN 3 5 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN 3 5 " --> pdb=" O VAL 31130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 16 through 20 removed outlier: 3.668A pdb=" N PHE 3 16 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 3 54 " --> pdb=" O LEU 3 40 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 62 through 68 removed outlier: 4.401A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE 3 87 " --> pdb=" O GLN 3 104 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN 3 104 " --> pdb=" O ILE 3 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE 3 89 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET 3 98 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AB2, first strand: chain '3' and resid 165 through 173 removed outlier: 5.654A pdb=" N VAL 3 167 " --> pdb=" O MET 3 187 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET 3 187 " --> pdb=" O VAL 3 167 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS 3 169 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU 3 208 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER 3 225 " --> pdb=" O LEU 3 208 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE 3 210 " --> pdb=" O LYS 3 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS 3 219 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 232 through 237 removed outlier: 4.492A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR 3 255 " --> pdb=" O SER 3 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 273 through 274 removed outlier: 6.353A pdb=" N ARG 3 273 " --> pdb=" O PHE 3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '3' and resid 287 through 294 removed outlier: 6.874A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE 3 310 " --> pdb=" O PHE 3 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 336 through 342 removed outlier: 3.690A pdb=" N ALA 3 338 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS 3 356 " --> pdb=" O GLU 3 400 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU 3 400 " --> pdb=" O HIS 3 356 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU 3 358 " --> pdb=" O VAL 3 398 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3' and resid 407 through 413 Processing sheet with id=AB8, first strand: chain '3' and resid 444 through 449 removed outlier: 6.379A pdb=" N ILE 3 764 " --> pdb=" O MET 3 447 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '3' and resid 461 through 462 removed outlier: 3.502A pdb=" N VAL 3 462 " --> pdb=" O TYR 3 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 507 through 510 removed outlier: 3.823A pdb=" N GLN 3 518 " --> pdb=" O ARG 3 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 546 through 548 removed outlier: 4.333A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 3 564 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 587 through 592 removed outlier: 3.617A pdb=" N SER 3 591 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA 3 606 " --> pdb=" O SER 3 591 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 637 through 643 removed outlier: 4.269A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS 3 641 " --> pdb=" O ASN 3 666 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 3 674 " --> pdb=" O THR 3 689 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 3 689 " --> pdb=" O LEU 3 674 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 700 through 706 removed outlier: 3.667A pdb=" N VAL 3 712 " --> pdb=" O SER 3 722 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 785 through 790 removed outlier: 7.111A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER 3 864 " --> pdb=" O GLN 3 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLN 3 881 " --> pdb=" O SER 3 864 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE 3 866 " --> pdb=" O LEU 3 879 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 3 879 " --> pdb=" O ILE 3 866 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 3 868 " --> pdb=" O LEU 3 877 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '3' and resid 886 through 894 removed outlier: 6.605A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '3' and resid 953 through 955 removed outlier: 6.823A pdb=" N LEU 3 967 " --> pdb=" O GLU 3 982 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU 3 982 " --> pdb=" O LEU 3 967 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL 3 969 " --> pdb=" O LYS 3 980 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 990 through 996 removed outlier: 3.731A pdb=" N GLY 3 992 " --> pdb=" O SER 31003 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE 31009 " --> pdb=" O ASP 31026 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP 31026 " --> pdb=" O PHE 31009 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP 31011 " --> pdb=" O PHE 31024 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '3' and resid 1033 through 1038 removed outlier: 4.372A pdb=" N THR 31035 " --> pdb=" O ALA 31047 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET 31093 " --> pdb=" O VAL 31055 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '4' and resid 39 through 43 Processing sheet with id=AD3, first strand: chain '4' and resid 131 through 132 removed outlier: 3.540A pdb=" N LYS 4 131 " --> pdb=" O PHE 4 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 282 through 283 removed outlier: 4.093A pdb=" N ALA C 282 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 406 through 408 removed outlier: 3.619A pdb=" N TYR C 414 " --> pdb=" O CYS C 408 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 362 through 363 removed outlier: 6.009A pdb=" N VAL E 526 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE E 559 " --> pdb=" O VAL E 526 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 528 " --> pdb=" O PHE E 559 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL E 449 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP E 529 " --> pdb=" O VAL E 449 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET E 451 " --> pdb=" O ASP E 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 593 through 599 removed outlier: 6.082A pdb=" N GLU E 594 " --> pdb=" O ALA E 719 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR E 721 " --> pdb=" O GLU E 594 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN E 596 " --> pdb=" O THR E 721 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE E 723 " --> pdb=" O GLN E 596 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE E 598 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 691 " --> pdb=" O TYR E 720 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE E 722 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN E 693 " --> pdb=" O PHE E 722 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 622 " --> pdb=" O LEU E 673 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA E 675 " --> pdb=" O VAL E 622 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE E 624 " --> pdb=" O ALA E 675 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET E 647 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 13 through 16 removed outlier: 4.137A pdb=" N ALA F 13 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG F 22 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP F 48 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 24 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 47 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE1, first strand: chain 'G' and resid 40 through 45 Processing sheet with id=AE2, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AE3, first strand: chain 'G' and resid 177 through 181 removed outlier: 3.651A pdb=" N GLU G 179 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 56 through 57 removed outlier: 3.840A pdb=" N GLN e 60 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS d 20 " --> pdb=" O ILE d 68 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU d 70 " --> pdb=" O SER d 18 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER d 18 " --> pdb=" O LEU d 70 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA d 72 " --> pdb=" O LYS d 16 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS d 16 " --> pdb=" O ALA d 72 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS d 26 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE d 30 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU d 44 " --> pdb=" O ILE d 30 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY d 58 " --> pdb=" O GLU d 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL d 46 " --> pdb=" O ASN d 56 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN d 56 " --> pdb=" O VAL d 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET d 48 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN d 54 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET d 59 " --> pdb=" O SER c 89 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER c 89 " --> pdb=" O MET d 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 86 " --> pdb=" O TRP c 34 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU c 35 " --> pdb=" O MET c 41 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N MET c 41 " --> pdb=" O LEU c 35 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS c 46 " --> pdb=" O ASP c 60 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP c 60 " --> pdb=" O CYS c 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL c 57 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET c 78 " --> pdb=" O VAL c 57 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP c 59 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG c 76 " --> pdb=" O ASP c 59 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA c 61 " --> pdb=" O LEU c 74 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG c 76 " --> pdb=" O GLY b 74 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY b 74 " --> pdb=" O ARG c 76 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE b 72 " --> pdb=" O MET c 78 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET b 27 " --> pdb=" O LEU b 23 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR b 32 " --> pdb=" O ASN b 46 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN b 46 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL b 34 " --> pdb=" O LEU b 44 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU b 44 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL b 36 " --> pdb=" O MET b 42 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N MET b 42 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN b 43 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL b 62 " --> pdb=" O GLN b 43 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA b 45 " --> pdb=" O GLY b 60 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY b 60 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR b 47 " --> pdb=" O HIS b 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS b 58 " --> pdb=" O THR b 47 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU b 49 " --> pdb=" O SER b 56 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG a 55 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN a 69 " --> pdb=" O ARG a 55 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS a 57 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU a 67 " --> pdb=" O LYS a 57 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER a 97 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS a 71 " --> pdb=" O TYR a 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR a 95 " --> pdb=" O LYS a 71 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET a 73 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP a 93 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR a 75 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN a 91 " --> pdb=" O THR a 75 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS a 98 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU g 70 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU g 13 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL g 25 " --> pdb=" O MET g 45 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET g 45 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY g 27 " --> pdb=" O VAL g 43 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL g 43 " --> pdb=" O GLY g 27 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS g 41 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS g 39 " --> pdb=" O SER g 59 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER g 59 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS g 41 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR g 57 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR g 57 " --> pdb=" O VAL f 82 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL f 82 " --> pdb=" O THR g 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER f 79 " --> pdb=" O ILE f 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR f 15 " --> pdb=" O PHE f 31 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR f 30 " --> pdb=" O ASP f 44 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP f 44 " --> pdb=" O THR f 30 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE f 41 " --> pdb=" O LEU f 72 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU f 72 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N CYS f 43 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL f 70 " --> pdb=" O CYS f 43 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU f 47 " --> pdb=" O VAL f 66 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL f 66 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU f 69 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS e 31 " --> pdb=" O ASN e 45 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN e 45 " --> pdb=" O LYS e 31 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE e 33 " --> pdb=" O MET e 43 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET e 43 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA e 35 " --> pdb=" O CYS e 41 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS e 41 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 129 through 136 removed outlier: 5.035A pdb=" N ILE O 129 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU O 150 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG O 131 " --> pdb=" O PHE O 148 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE O 148 " --> pdb=" O ARG O 131 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS O 133 " --> pdb=" O TYR O 146 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR O 146 " --> pdb=" O HIS O 133 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL O 135 " --> pdb=" O ARG O 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 168 through 169 Processing sheet with id=AE7, first strand: chain 'm' and resid 54 through 58 removed outlier: 6.589A pdb=" N GLU m 49 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS m 58 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR m 47 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG i 55 " --> pdb=" O ASN i 69 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN i 69 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS i 57 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU i 67 " --> pdb=" O LYS i 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE i 59 " --> pdb=" O MET i 65 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET i 65 " --> pdb=" O PHE i 59 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL i 66 " --> pdb=" O PHE i 100 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE i 100 " --> pdb=" O VAL i 66 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU i 68 " --> pdb=" O LYS i 98 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS i 98 " --> pdb=" O GLU i 68 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL h 25 " --> pdb=" O MET h 45 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET h 45 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY h 27 " --> pdb=" O VAL h 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL h 43 " --> pdb=" O GLY h 27 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE h 29 " --> pdb=" O LYS h 41 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS h 41 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS h 39 " --> pdb=" O SER h 59 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER h 59 " --> pdb=" O HIS h 39 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS h 41 " --> pdb=" O THR h 57 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR h 57 " --> pdb=" O LYS h 41 " (cutoff:3.500A) removed outlier: 14.009A pdb=" N LEU h 55 " --> pdb=" O GLY k 84 " (cutoff:3.500A) removed outlier: 12.445A pdb=" N GLY k 84 " --> pdb=" O LEU h 55 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR h 57 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL k 82 " --> pdb=" O THR h 57 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG k 16 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR k 30 " --> pdb=" O ASP k 44 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP k 44 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS k 32 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU k 42 " --> pdb=" O LYS k 32 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE k 34 " --> pdb=" O LEU k 40 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU k 40 " --> pdb=" O PHE k 34 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE k 41 " --> pdb=" O LEU k 72 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU k 72 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS k 43 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL k 70 " --> pdb=" O CYS k 43 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU k 47 " --> pdb=" O VAL k 66 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL k 66 " --> pdb=" O GLU k 47 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU k 69 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE j 70 " --> pdb=" O GLU j 21 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR j 28 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL j 48 " --> pdb=" O TYR j 28 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY j 30 " --> pdb=" O ILE j 46 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE j 46 " --> pdb=" O GLY j 30 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU j 32 " --> pdb=" O SER j 44 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER j 44 " --> pdb=" O LEU j 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU j 34 " --> pdb=" O GLN j 42 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU j 59 " --> pdb=" O ASN j 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR j 47 " --> pdb=" O GLN j 57 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN j 57 " --> pdb=" O THR j 47 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR j 49 " --> pdb=" O VAL j 55 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL j 55 " --> pdb=" O THR j 49 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN j 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE n 30 " --> pdb=" O GLU n 44 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU n 44 " --> pdb=" O ILE n 30 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG n 32 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE n 42 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE n 34 " --> pdb=" O LEU n 40 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU n 40 " --> pdb=" O PHE n 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY n 58 " --> pdb=" O GLU n 44 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL n 46 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN n 56 " --> pdb=" O VAL n 46 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N MET n 59 " --> pdb=" O SER l 89 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER l 89 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG l 42 " --> pdb=" O GLU l 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU l 63 " --> pdb=" O ARG l 42 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU l 44 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA l 61 " --> pdb=" O GLU l 44 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS l 46 " --> pdb=" O ASP l 59 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL l 57 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP l 60 " --> pdb=" O GLY l 75 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY l 75 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU l 62 " --> pdb=" O GLN l 73 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN l 73 " --> pdb=" O GLU l 62 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE l 64 " --> pdb=" O ARG l 71 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG l 71 " --> pdb=" O ILE l 64 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG l 76 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY m 74 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR m 32 " --> pdb=" O ASN m 46 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN m 46 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL m 34 " --> pdb=" O LEU m 44 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU m 44 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL m 36 " --> pdb=" O MET m 42 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET m 42 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'k' and resid 50 through 51 Processing sheet with id=AE9, first strand: chain 'M' and resid 40 through 45 Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.605A pdb=" N THR N 11 " --> pdb=" O CYS N 6 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '6' and resid 18 through 19 removed outlier: 4.250A pdb=" N ALA 6 18 " --> pdb=" O ILE 6 45 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '6' and resid 21 through 22 Processing sheet with id=AF4, first strand: chain '6' and resid 39 through 42 removed outlier: 6.406A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) 1962 hydrogen bonds defined for protein. 5535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 210 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 157 stacking parallelities Total time for adding SS restraints: 13.86 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 7076 1.27 - 1.41: 11451 1.41 - 1.55: 25047 1.55 - 1.69: 785 1.69 - 1.84: 261 Bond restraints: 44620 Sorted by residual: bond pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.04e+02 bond pdb=" C ARG 6 38 " pdb=" N PRO 6 39 " ideal model delta sigma weight residual 1.332 1.517 -0.185 1.33e-02 5.65e+03 1.94e+02 bond pdb=" N PRO 1 718 " pdb=" CA PRO 1 718 " ideal model delta sigma weight residual 1.468 1.660 -0.192 1.70e-02 3.46e+03 1.28e+02 bond pdb=" C CYS 6 30 " pdb=" O CYS 6 30 " ideal model delta sigma weight residual 1.234 1.125 0.109 1.27e-02 6.20e+03 7.32e+01 bond pdb=" C VAL O 176 " pdb=" O VAL O 176 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.04e-02 9.25e+03 6.30e+01 ... (remaining 44615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.20: 60825 6.20 - 12.41: 295 12.41 - 18.61: 22 18.61 - 24.82: 2 24.82 - 31.02: 2 Bond angle restraints: 61146 Sorted by residual: angle pdb=" N ASP 31064 " pdb=" CA ASP 31064 " pdb=" CB ASP 31064 " ideal model delta sigma weight residual 110.49 141.51 -31.02 1.69e+00 3.50e-01 3.37e+02 angle pdb=" C GLY C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta sigma weight residual 119.84 139.93 -20.09 1.25e+00 6.40e-01 2.58e+02 angle pdb=" N PRO 1 780 " pdb=" CA PRO 1 780 " pdb=" C PRO 1 780 " ideal model delta sigma weight residual 113.40 133.41 -20.01 1.34e+00 5.57e-01 2.23e+02 angle pdb=" C ARG 6 38 " pdb=" N PRO 6 39 " pdb=" CA PRO 6 39 " ideal model delta sigma weight residual 119.89 133.85 -13.96 1.02e+00 9.61e-01 1.87e+02 angle pdb=" C4' U H 69 " pdb=" C3' U H 69 " pdb=" O3' U H 69 " ideal model delta sigma weight residual 113.00 130.89 -17.89 1.50e+00 4.44e-01 1.42e+02 ... (remaining 61141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 23233 34.79 - 69.58: 1467 69.58 - 104.37: 150 104.37 - 139.16: 16 139.16 - 173.95: 10 Dihedral angle restraints: 24876 sinusoidal: 12311 harmonic: 12565 Sorted by residual: dihedral pdb=" C4' U L 90 " pdb=" C3' U L 90 " pdb=" C2' U L 90 " pdb=" C1' U L 90 " ideal model delta sinusoidal sigma weight residual -35.00 36.06 -71.06 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' U L 90 " pdb=" C4' U L 90 " pdb=" C3' U L 90 " pdb=" O3' U L 90 " ideal model delta sinusoidal sigma weight residual 147.00 83.59 63.41 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' C L 73 " pdb=" C1' C L 73 " pdb=" N1 C L 73 " pdb=" C2 C L 73 " ideal model delta sinusoidal sigma weight residual 200.00 41.62 158.38 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 24873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.055: 6008 1.055 - 2.110: 0 2.110 - 3.165: 0 3.165 - 4.221: 0 4.221 - 5.276: 5 Chirality restraints: 6013 Sorted by residual: chirality pdb=" C22 SJT 6 204 " pdb=" C21 SJT 6 204 " pdb=" C23 SJT 6 204 " pdb=" C24 SJT 6 204 " both_signs ideal model delta sigma weight residual False 2.75 -2.53 5.28 2.00e-01 2.50e+01 6.96e+02 chirality pdb=" C25 SJT 6 204 " pdb=" C24 SJT 6 204 " pdb=" C26 SJT 6 204 " pdb=" O6 SJT 6 204 " both_signs ideal model delta sigma weight residual False 2.51 -2.56 5.06 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C3 SJT 6 204 " pdb=" C2 SJT 6 204 " pdb=" C4 SJT 6 204 " pdb=" O1 SJT 6 204 " both_signs ideal model delta sigma weight residual False 2.61 -2.41 5.02 2.00e-01 2.50e+01 6.31e+02 ... (remaining 6010 not shown) Planarity restraints: 7428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 SJT 6 204 " -0.316 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C15 SJT 6 204 " 0.486 2.00e-02 2.50e+03 pdb=" C16 SJT 6 204 " 0.075 2.00e-02 2.50e+03 pdb=" C17 SJT 6 204 " -0.113 2.00e-02 2.50e+03 pdb=" C18 SJT 6 204 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJT 6 204 " 0.245 2.00e-02 2.50e+03 1.46e-01 2.68e+02 pdb=" C SJT 6 204 " 0.028 2.00e-02 2.50e+03 pdb=" O SJT 6 204 " 0.025 2.00e-02 2.50e+03 pdb=" C1 SJT 6 204 " -0.126 2.00e-02 2.50e+03 pdb=" C7 SJT 6 204 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 SJT 6 204 " -0.084 2.00e-02 2.50e+03 1.54e-01 2.38e+02 pdb=" C18 SJT 6 204 " 0.198 2.00e-02 2.50e+03 pdb=" C19 SJT 6 204 " -0.202 2.00e-02 2.50e+03 pdb=" C20 SJT 6 204 " 0.088 2.00e-02 2.50e+03 ... (remaining 7425 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 31 1.79 - 2.57: 438 2.57 - 3.35: 49518 3.35 - 4.12: 105099 4.12 - 4.90: 173903 Nonbonded interactions: 328989 Sorted by model distance: nonbonded pdb=" O4 U L 30 " pdb=" CD1 LEU O 175 " model vdw 1.018 3.460 nonbonded pdb=" O THR O 62 " pdb=" N GLU O 64 " model vdw 1.051 3.120 nonbonded pdb=" O2' G L 164 " pdb=" N ARG h 50 " model vdw 1.115 3.120 nonbonded pdb=" C8 A L 118 " pdb=" N PRO N 2 " model vdw 1.143 3.340 nonbonded pdb=" O2' G L 164 " pdb=" C ASN h 49 " model vdw 1.231 3.270 ... (remaining 328984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 19 through 77 or resid 88 through 114)) selection = (chain 'i' and ((resid 19 through 27 and (name N or name CA or name C or name O \ )) or resid 28 or (resid 29 through 88 and (name N or name CA or name C or name \ O )) or resid 89 or (resid 90 through 112 and (name N or name CA or name C or na \ me O )) or resid 113 or (resid 114 and (name N or name CA or name C or name O )) \ )) } ncs_group { reference = chain 'b' selection = (chain 'm' and ((resid 2 through 3 and (name N or name CA or name C or name O )) \ or resid 4 or (resid 5 through 6 and (name N or name CA or name C or name O )) \ or resid 7 or (resid 8 and (name N or name CA or name C or name O )) or resid 9 \ or (resid 10 through 17 and (name N or name CA or name C or name O )) or resid 1 \ 8 or (resid 19 through 75 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'c' and resid 14 through 90) selection = (chain 'l' and ((resid 14 through 16 and (name N or name CA or name C or name O \ )) or resid 17 or (resid 18 through 90 and (name N or name CA or name C or name \ O )))) } ncs_group { reference = (chain 'd' and resid 4 through 76) selection = (chain 'n' and ((resid 4 through 5 and (name N or name CA or name C or name O )) \ or resid 6 through 7 or (resid 8 through 35 and (name N or name CA or name C or \ name O )) or resid 36 or (resid 37 through 76 and (name N or name CA or name C \ or name O )))) } ncs_group { reference = (chain 'e' and resid 3 through 83) selection = (chain 'j' and ((resid 3 through 5 and (name N or name CA or name C or name O )) \ or resid 6 or (resid 7 through 73 and (name N or name CA or name C or name O )) \ or resid 74 or (resid 75 through 80 and (name N or name CA or name C or name O \ )) or resid 81 or (resid 82 through 83 and (name N or name CA or name C or name \ O )))) } ncs_group { reference = (chain 'g' and resid 2 through 82) selection = (chain 'h' and ((resid 2 through 51 and (name N or name CA or name C or name O ) \ ) or resid 52 or (resid 53 through 70 and (name N or name CA or name C or name O \ )) or resid 71 or (resid 72 through 74 and (name N or name CA or name C or name \ O )) or resid 75 or (resid 76 through 82 and (name N or name CA or name C or na \ me O )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.160 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: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 47.660 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3638 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 0.468 44643 Z= 0.629 Angle : 1.308 31.021 61160 Z= 0.842 Chirality : 0.169 5.276 6013 Planarity : 0.009 0.273 7428 Dihedral : 19.774 173.952 17992 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.47 % Favored : 96.22 % Rotamer: Outliers : 7.75 % Allowed : 17.35 % Favored : 74.90 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % Twisted General : 0.02 % 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: -2.52 (0.10), residues: 5499 helix: -1.53 (0.10), residues: 1877 sheet: -0.94 (0.15), residues: 1170 loop : -2.07 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG n 63 TYR 0.051 0.004 TYR 6 36 PHE 0.052 0.004 PHE O 48 TRP 0.055 0.004 TRP O 187 HIS 0.056 0.003 HIS i 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.59 (44620) covalent geometry : angle 1.29181 / 0.84 (61146) hydrogen bonds : bond 0.16623 / 13.18 ( 2164) hydrogen bonds : angle 7.33597 / 8.29 ( 5923) metal coordination : bond 0.22932 / 12.82 ( 22) metal coordination : angle 13.60597 / 8.31 ( 14) Misc. bond : bond 0.31447 / 16.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 602 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 699 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5463 (tm-30) REVERT: 1 869 MET cc_start: 0.6007 (tpt) cc_final: 0.5743 (tpt) REVERT: 1 910 MET cc_start: 0.4240 (mmt) cc_final: 0.3905 (mmp) REVERT: 2 587 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.6141 (p-80) REVERT: 3 645 MET cc_start: -0.1672 (tmt) cc_final: -0.2542 (tpp) REVERT: 3 664 TYR cc_start: 0.7573 (m-80) cc_final: 0.6991 (m-80) REVERT: C 464 LEU cc_start: 0.7491 (tt) cc_final: 0.7190 (mt) REVERT: E 199 SER cc_start: 0.3705 (t) cc_final: 0.3373 (t) REVERT: O 3 GLN cc_start: 0.0719 (OUTLIER) cc_final: -0.0733 (pt0) REVERT: k 38 MET cc_start: 0.2469 (mmm) cc_final: 0.1978 (mmm) REVERT: M 61 GLU cc_start: 0.0713 (OUTLIER) cc_final: 0.0490 (mm-30) REVERT: l 41 MET cc_start: 0.2191 (ttp) cc_final: 0.0612 (tpt) REVERT: i 114 LEU cc_start: -0.0262 (OUTLIER) cc_final: -0.0858 (mp) REVERT: N 48 SER cc_start: -0.0531 (OUTLIER) cc_final: -0.0737 (p) REVERT: j 78 LYS cc_start: 0.1877 (OUTLIER) cc_final: 0.1585 (ttmm) REVERT: j 83 LEU cc_start: 0.0979 (OUTLIER) cc_final: 0.0659 (mp) outliers start: 237 outliers final: 56 residues processed: 807 average time/residue: 0.6675 time to fit residues: 672.7832 Evaluate side-chains 408 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 344 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 699 GLN Chi-restraints excluded: chain 1 residue 721 ILE Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 965 CYS Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1137 ARG Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1191 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain k residue 12 HIS Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 58 GLN Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain M residue 8 PRO Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 68 THR Chi-restraints excluded: chain l residue 70 SER Chi-restraints excluded: chain l residue 80 LYS Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain i residue 37 LYS Chi-restraints excluded: chain i residue 51 LYS Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 78 LYS Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 61 CYS Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 50.0000 chunk 265 optimal weight: 50.0000 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 662 HIS ** 1 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 901 GLN ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 919 ASN ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11002 ASN 11069 HIS 11144 GLN 11252 GLN 2 458 ASN 2 467 GLN 2 490 HIS 3 27 GLN 3 138 GLN ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 254 ASN 3 264 GLN 3 480 ASN 3 612 ASN 3 636 GLN 3 749 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 916 ASN 31020 GLN 31083 ASN C 400 HIS C 445 HIS C 448 ASN O 35 ASN O 96 ASN h 49 ASN k 37 HIS k 76 ASN 6 55 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.274350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.227938 restraints weight = 79324.271| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 3.64 r_work: 0.4134 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.197 44643 Z= 0.549 Angle : 1.230 26.095 61160 Z= 0.645 Chirality : 0.078 1.772 6013 Planarity : 0.010 0.127 7428 Dihedral : 18.500 176.457 11063 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.89 % Favored : 94.85 % Rotamer: Outliers : 9.80 % Allowed : 20.72 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % Twisted General : 0.06 % 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: -2.19 (0.10), residues: 5499 helix: -0.92 (0.11), residues: 1917 sheet: -0.94 (0.15), residues: 1143 loop : -2.09 (0.11), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG 3 128 TYR 0.066 0.006 TYR 3 926 PHE 0.075 0.007 PHE 5 66 TRP 0.057 0.007 TRP 3 903 HIS 0.027 0.004 HIS C 400 Details of bonding type rmsd/Z covalent geometry : bond 0.01288 / 0.55 (44620) covalent geometry : angle 1.22758 / 0.64 (61146) hydrogen bonds : bond 0.07836 / 6.13 ( 2164) hydrogen bonds : angle 5.99332 / 6.41 ( 5923) metal coordination : bond 0.03508 / 2.10 ( 22) metal coordination : angle 4.84393 / 2.96 ( 14) Misc. bond : bond 0.02307 / 1.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 347 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4850 (m-80) cc_final: 0.4050 (m-10) REVERT: 1 538 LEU cc_start: 0.7972 (tp) cc_final: 0.7660 (mp) REVERT: 1 623 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.4813 (t80) REVERT: 1 760 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6285 (tm-30) REVERT: 1 763 ASN cc_start: 0.7034 (t0) cc_final: 0.6614 (m-40) REVERT: 1 816 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7507 (ttpp) REVERT: 1 874 LYS cc_start: 0.7387 (mttt) cc_final: 0.6944 (mtmt) REVERT: 1 919 ASN cc_start: 0.8079 (m110) cc_final: 0.7732 (p0) REVERT: 1 1013 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5372 (mt) REVERT: 1 1106 ARG cc_start: 0.4645 (OUTLIER) cc_final: 0.4386 (ttt180) REVERT: 1 1156 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5717 (tp30) REVERT: 1 1221 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: 1 1267 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6298 (ptpp) REVERT: 2 500 VAL cc_start: 0.6531 (OUTLIER) cc_final: 0.6241 (m) REVERT: 2 514 LYS cc_start: 0.3951 (OUTLIER) cc_final: 0.3219 (pmmt) REVERT: 2 706 THR cc_start: 0.5881 (OUTLIER) cc_final: 0.5661 (p) REVERT: 3 10 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8221 (mmt-90) REVERT: 3 49 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7969 (mppt) REVERT: 3 131 MET cc_start: 0.7236 (ttm) cc_final: 0.6997 (ttm) REVERT: 3 273 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.6044 (mtp180) REVERT: 3 278 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5716 (pt) REVERT: 3 331 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: 3 386 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6448 (m-80) REVERT: 3 390 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.3977 (ptt90) REVERT: 3 475 ILE cc_start: 0.4380 (OUTLIER) cc_final: 0.4004 (tp) REVERT: 3 573 GLN cc_start: 0.4923 (OUTLIER) cc_final: 0.4449 (mm110) REVERT: 3 574 LEU cc_start: 0.1324 (OUTLIER) cc_final: 0.1069 (tt) REVERT: 3 645 MET cc_start: -0.0907 (tmt) cc_final: -0.1851 (tpp) REVERT: 3 688 ASP cc_start: 0.4083 (OUTLIER) cc_final: 0.3557 (t0) REVERT: 3 776 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.4896 (pt0) REVERT: 3 795 ASN cc_start: 0.6505 (m-40) cc_final: 0.6046 (p0) REVERT: 3 1117 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7975 (mp) REVERT: 3 1148 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8476 (mp) REVERT: 3 1186 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: C 440 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (pt) REVERT: E 157 GLU cc_start: 0.6639 (pp20) cc_final: 0.6269 (tp30) REVERT: E 160 MET cc_start: 0.2986 (OUTLIER) cc_final: 0.2374 (mpm) REVERT: E 197 LYS cc_start: 0.4173 (OUTLIER) cc_final: 0.3805 (mptp) REVERT: E 233 GLU cc_start: 0.2670 (OUTLIER) cc_final: 0.2427 (tt0) REVERT: O 52 ARG cc_start: 0.3193 (OUTLIER) cc_final: 0.2769 (mtm-85) REVERT: O 168 LYS cc_start: -0.2559 (OUTLIER) cc_final: -0.2961 (mmmt) REVERT: M 61 GLU cc_start: 0.0593 (OUTLIER) cc_final: 0.0302 (mm-30) REVERT: n 69 MET cc_start: 0.1482 (ptm) cc_final: -0.0242 (pmm) REVERT: l 41 MET cc_start: 0.2931 (ttp) cc_final: 0.0252 (tpt) REVERT: l 80 LYS cc_start: 0.1431 (OUTLIER) cc_final: 0.0541 (mptt) REVERT: l 86 LEU cc_start: 0.0553 (OUTLIER) cc_final: 0.0299 (tp) REVERT: i 114 LEU cc_start: -0.1478 (OUTLIER) cc_final: -0.2110 (mp) outliers start: 300 outliers final: 105 residues processed: 602 average time/residue: 0.6386 time to fit residues: 486.5924 Evaluate side-chains 436 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 297 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain 1 residue 556 ILE Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 683 LEU Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 723 SER Chi-restraints excluded: chain 1 residue 771 LEU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 816 LYS Chi-restraints excluded: chain 1 residue 821 HIS Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 914 PHE Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1030 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1062 LEU Chi-restraints excluded: chain 1 residue 1106 ARG Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1221 GLU Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 500 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 511 LEU Chi-restraints excluded: chain 2 residue 514 LYS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 49 LYS Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 66 MET Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 237 THR Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 267 ILE Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 386 PHE Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 393 LYS Chi-restraints excluded: chain 3 residue 419 ASP Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 468 ASP Chi-restraints excluded: chain 3 residue 475 ILE Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 688 ASP Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 776 GLN Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 790 ILE Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 914 ILE Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1115 GLU Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1117 LEU Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1148 LEU Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1186 GLU Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain 5 residue 74 GLN Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 52 ARG Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain k residue 58 GLN Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 80 LYS Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain 6 residue 22 LEU Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 47 ASP Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 76 THR Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 19 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 570 optimal weight: 20.0000 chunk 242 optimal weight: 0.5980 chunk 392 optimal weight: 0.9990 chunk 527 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 chunk 475 optimal weight: 50.0000 chunk 170 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 305 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN ** 1 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 587 HIS 3 138 GLN 3 194 ASN 3 254 ASN 3 422 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 861 GLN C 448 ASN O 96 ASN k 58 GLN n 26 HIS i 62 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.279501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.236070 restraints weight = 79704.383| |-----------------------------------------------------------------------------| r_work (start): 0.4774 rms_B_bonded: 3.31 r_work: 0.4187 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44643 Z= 0.152 Angle : 0.723 27.177 61160 Z= 0.365 Chirality : 0.057 1.979 6013 Planarity : 0.005 0.071 7428 Dihedral : 17.980 179.247 10982 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 6.24 % Allowed : 24.05 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -1.03 (0.11), residues: 5499 helix: 0.55 (0.12), residues: 1898 sheet: -0.64 (0.15), residues: 1145 loop : -1.68 (0.11), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 216 TYR 0.026 0.002 TYR 3 970 PHE 0.085 0.002 PHE 1 914 TRP 0.019 0.002 TRP 1 732 HIS 0.008 0.001 HIS 1 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (44620) covalent geometry : angle 0.72050 / 0.36 (61146) hydrogen bonds : bond 0.04638 / 3.71 ( 2164) hydrogen bonds : angle 4.97230 / 5.33 ( 5923) metal coordination : bond 0.01379 / 0.91 ( 22) metal coordination : angle 4.02641 / 2.69 ( 14) Misc. bond : bond 0.00505 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 321 time to evaluate : 1.583 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: B 45 TYR cc_start: 0.4766 (m-80) cc_final: 0.4363 (m-10) REVERT: B 47 MET cc_start: 0.2690 (OUTLIER) cc_final: 0.2231 (mtp) REVERT: B 55 GLU cc_start: 0.3928 (OUTLIER) cc_final: 0.3676 (pt0) REVERT: 1 538 LEU cc_start: 0.7959 (tp) cc_final: 0.7649 (mp) REVERT: 1 623 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4977 (t80) REVERT: 1 698 GLN cc_start: 0.6113 (mm-40) cc_final: 0.5780 (tm130) REVERT: 1 964 THR cc_start: 0.8038 (p) cc_final: 0.7801 (t) REVERT: 1 1009 MET cc_start: 0.7614 (tpp) cc_final: 0.7257 (tpp) REVERT: 1 1287 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7484 (mp) REVERT: 2 529 LYS cc_start: 0.7720 (tttp) cc_final: 0.7111 (ptpt) REVERT: 2 706 THR cc_start: 0.5403 (OUTLIER) cc_final: 0.5183 (p) REVERT: 3 278 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5641 (pt) REVERT: 3 331 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: 3 368 ASP cc_start: 0.3674 (OUTLIER) cc_final: 0.2472 (p0) REVERT: 3 525 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4694 (ptp-170) REVERT: 3 573 GLN cc_start: 0.4843 (OUTLIER) cc_final: 0.4403 (mm110) REVERT: 3 645 MET cc_start: -0.1049 (tmt) cc_final: -0.1808 (tpp) REVERT: 3 812 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5636 (mtmm) REVERT: 3 936 LYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5766 (ptmm) REVERT: 3 1016 ARG cc_start: 0.4235 (OUTLIER) cc_final: 0.3715 (tpt170) REVERT: E 157 GLU cc_start: 0.6814 (pp20) cc_final: 0.6494 (pp20) REVERT: E 158 GLU cc_start: 0.6262 (tm-30) cc_final: 0.6015 (tm-30) REVERT: E 160 MET cc_start: 0.2455 (OUTLIER) cc_final: 0.1117 (mpm) REVERT: E 165 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5323 (pp20) REVERT: E 166 ARG cc_start: 0.2023 (mtm180) cc_final: 0.1609 (mtm180) REVERT: E 198 TRP cc_start: 0.5129 (OUTLIER) cc_final: 0.3937 (p90) REVERT: E 235 VAL cc_start: 0.4119 (OUTLIER) cc_final: 0.3747 (t) REVERT: O 168 LYS cc_start: -0.2749 (OUTLIER) cc_final: -0.3062 (mmmt) REVERT: n 59 MET cc_start: -0.1197 (ttm) cc_final: -0.1668 (tpt) REVERT: l 41 MET cc_start: 0.2704 (ttp) cc_final: 0.0283 (tpt) REVERT: l 80 LYS cc_start: 0.0679 (OUTLIER) cc_final: 0.0201 (mptt) REVERT: i 73 MET cc_start: 0.2112 (OUTLIER) cc_final: 0.1902 (ttm) REVERT: i 114 LEU cc_start: -0.1014 (OUTLIER) cc_final: -0.1529 (mp) REVERT: j 43 MET cc_start: 0.2154 (OUTLIER) cc_final: 0.1027 (ttt) REVERT: j 46 ILE cc_start: -0.0132 (OUTLIER) cc_final: -0.0655 (tp) outliers start: 191 outliers final: 73 residues processed: 475 average time/residue: 0.6117 time to fit residues: 373.0987 Evaluate side-chains 385 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1231 MET Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 483 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 512 GLN Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 220 VAL Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 368 ASP Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 762 LEU Chi-restraints excluded: chain 3 residue 812 LYS Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 80 LYS Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain i residue 37 LYS Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 449 optimal weight: 40.0000 chunk 276 optimal weight: 30.0000 chunk 472 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 498 optimal weight: 40.0000 chunk 327 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 267 optimal weight: 20.0000 chunk 132 optimal weight: 0.0050 chunk 227 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 599 ASN 1 763 ASN ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 587 HIS 3 28 GLN 3 219 HIS 3 231 HIS 3 422 GLN ** 3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 844 ASN 3 994 GLN C 448 ASN k 12 HIS l 19 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.276364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.228072 restraints weight = 79465.728| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 3.19 r_work: 0.4211 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 44643 Z= 0.146 Angle : 0.691 27.063 61160 Z= 0.340 Chirality : 0.056 1.973 6013 Planarity : 0.005 0.062 7428 Dihedral : 17.762 177.322 10964 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 5.65 % Allowed : 24.93 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -0.58 (0.11), residues: 5499 helix: 1.07 (0.12), residues: 1912 sheet: -0.52 (0.15), residues: 1157 loop : -1.49 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 3 390 TYR 0.027 0.002 TYR 3 970 PHE 0.037 0.002 PHE 1 914 TRP 0.013 0.002 TRP 1 732 HIS 0.007 0.001 HIS 1 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (44620) covalent geometry : angle 0.68171 / 0.34 (61146) hydrogen bonds : bond 0.04156 / 3.28 ( 2164) hydrogen bonds : angle 4.66862 / 4.99 ( 5923) metal coordination : bond 0.02173 / 1.39 ( 22) metal coordination : angle 7.48894 / 4.21 ( 14) Misc. bond : bond 0.00409 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 306 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4898 (m-80) cc_final: 0.4464 (m-10) REVERT: B 47 MET cc_start: 0.2487 (OUTLIER) cc_final: 0.2129 (mtp) REVERT: 1 538 LEU cc_start: 0.8010 (tp) cc_final: 0.7693 (mp) REVERT: 1 623 TYR cc_start: 0.5760 (OUTLIER) cc_final: 0.4990 (t80) REVERT: 1 799 ASP cc_start: 0.7073 (p0) cc_final: 0.6865 (p0) REVERT: 1 964 THR cc_start: 0.8005 (p) cc_final: 0.7795 (t) REVERT: 1 1000 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6658 (mp) REVERT: 1 1241 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7825 (tt) REVERT: 1 1287 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7594 (mp) REVERT: 2 529 LYS cc_start: 0.7799 (tttp) cc_final: 0.7099 (ptmt) REVERT: 3 219 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.6320 (p90) REVERT: 3 273 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.6143 (mtp180) REVERT: 3 278 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6236 (mt) REVERT: 3 331 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: 3 525 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4647 (ptp-170) REVERT: 3 573 GLN cc_start: 0.5126 (OUTLIER) cc_final: 0.4715 (mm110) REVERT: 3 583 MET cc_start: -0.2942 (mmt) cc_final: -0.3312 (mtt) REVERT: 3 645 MET cc_start: -0.0868 (tmt) cc_final: -0.1670 (tpp) REVERT: 3 1016 ARG cc_start: 0.4763 (OUTLIER) cc_final: 0.4263 (tpt170) REVERT: 3 1105 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: 3 1151 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7429 (mt-10) REVERT: E 160 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.1639 (mmt) REVERT: E 198 TRP cc_start: 0.5562 (OUTLIER) cc_final: 0.4655 (p90) REVERT: E 235 VAL cc_start: 0.4093 (OUTLIER) cc_final: 0.3725 (t) REVERT: O 58 THR cc_start: -0.1902 (OUTLIER) cc_final: -0.2187 (t) REVERT: O 168 LYS cc_start: -0.2448 (OUTLIER) cc_final: -0.2806 (mmmt) REVERT: n 59 MET cc_start: -0.1287 (ttm) cc_final: -0.1792 (tpt) REVERT: n 69 MET cc_start: 0.1392 (ptm) cc_final: -0.0585 (pmm) REVERT: l 41 MET cc_start: 0.2674 (ttp) cc_final: 0.0401 (tpt) REVERT: i 114 LEU cc_start: -0.0505 (OUTLIER) cc_final: -0.1133 (mp) REVERT: N 3 LYS cc_start: 0.0092 (OUTLIER) cc_final: -0.0419 (tmtt) REVERT: j 46 ILE cc_start: 0.0078 (OUTLIER) cc_final: -0.0147 (tp) outliers start: 173 outliers final: 84 residues processed: 445 average time/residue: 0.6181 time to fit residues: 353.1952 Evaluate side-chains 393 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 288 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 624 VAL Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 821 HIS Chi-restraints excluded: chain 1 residue 886 HIS Chi-restraints excluded: chain 1 residue 914 PHE Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1000 ILE Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1231 MET Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 483 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 220 VAL Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 762 LEU Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1105 GLN Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 533 optimal weight: 20.0000 chunk 264 optimal weight: 40.0000 chunk 67 optimal weight: 0.9980 chunk 465 optimal weight: 50.0000 chunk 430 optimal weight: 4.9990 chunk 539 optimal weight: 9.9990 chunk 428 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 254 optimal weight: 0.0010 chunk 94 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 912 ASN ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN 3 422 GLN ** 3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 749 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 14 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.274819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.227066 restraints weight = 78560.746| |-----------------------------------------------------------------------------| r_work (start): 0.4710 rms_B_bonded: 3.39 r_work: 0.4126 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 44643 Z= 0.271 Angle : 0.815 27.430 61160 Z= 0.408 Chirality : 0.060 1.979 6013 Planarity : 0.006 0.069 7428 Dihedral : 17.727 178.673 10954 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 6.86 % Allowed : 24.67 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: -0.70 (0.11), residues: 5499 helix: 0.98 (0.12), residues: 1900 sheet: -0.60 (0.15), residues: 1175 loop : -1.56 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 163 TYR 0.059 0.003 TYR 3 970 PHE 0.043 0.003 PHE 3 261 TRP 0.023 0.003 TRP 3 903 HIS 0.022 0.002 HIS 3 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (44620) covalent geometry : angle 0.80468 / 0.41 (61146) hydrogen bonds : bond 0.04983 / 3.83 ( 2164) hydrogen bonds : angle 4.89414 / 5.25 ( 5923) metal coordination : bond 0.01594 / 1.04 ( 22) metal coordination : angle 8.70502 / 4.87 ( 14) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 284 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.5021 (m-80) cc_final: 0.4720 (m-10) REVERT: B 47 MET cc_start: 0.2702 (OUTLIER) cc_final: 0.2440 (mtp) REVERT: 1 538 LEU cc_start: 0.8140 (tp) cc_final: 0.7773 (mp) REVERT: 1 623 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.5082 (t80) REVERT: 1 684 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7675 (tpm-80) REVERT: 1 714 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: 1 1056 MET cc_start: 0.8059 (mtm) cc_final: 0.7832 (mtp) REVERT: 1 1156 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5374 (tp30) REVERT: 1 1193 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6569 (tt0) REVERT: 1 1287 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7737 (mp) REVERT: 2 502 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: 2 529 LYS cc_start: 0.7839 (tttp) cc_final: 0.7220 (ptmt) REVERT: 3 66 MET cc_start: 0.9102 (mmm) cc_final: 0.8782 (tpt) REVERT: 3 273 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6454 (mtp180) REVERT: 3 274 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5887 (mtm-85) REVERT: 3 278 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7253 (mt) REVERT: 3 331 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: 3 400 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: 3 525 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.4576 (ptp-170) REVERT: 3 640 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7166 (pt) REVERT: 3 645 MET cc_start: -0.0425 (tmt) cc_final: -0.0762 (tpt) REVERT: 3 936 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.6045 (ptmm) REVERT: 3 1001 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8014 (mm) REVERT: 3 1016 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4451 (tpt170) REVERT: E 198 TRP cc_start: 0.5705 (OUTLIER) cc_final: 0.4475 (p90) REVERT: E 235 VAL cc_start: 0.4492 (OUTLIER) cc_final: 0.4289 (t) REVERT: O 168 LYS cc_start: -0.2543 (OUTLIER) cc_final: -0.2900 (mmmt) REVERT: n 59 MET cc_start: -0.1110 (ttm) cc_final: -0.1640 (tpt) REVERT: l 41 MET cc_start: 0.2265 (ttp) cc_final: 0.0052 (tpt) REVERT: i 114 LEU cc_start: -0.0772 (OUTLIER) cc_final: -0.1080 (mt) REVERT: N 3 LYS cc_start: 0.0071 (OUTLIER) cc_final: -0.0507 (tmtt) REVERT: j 46 ILE cc_start: 0.0088 (OUTLIER) cc_final: -0.0154 (tp) outliers start: 210 outliers final: 105 residues processed: 461 average time/residue: 0.5960 time to fit residues: 355.9892 Evaluate side-chains 403 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 275 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 687 VAL Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 821 HIS Chi-restraints excluded: chain 1 residue 886 HIS Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1096 THR Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1193 GLN Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 483 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 512 GLN Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 762 LEU Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 799 ILE Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 895 ARG Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1058 LEU Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 14 MET Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 14 optimal weight: 50.0000 chunk 205 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 418 optimal weight: 50.0000 chunk 476 optimal weight: 50.0000 chunk 474 optimal weight: 50.0000 chunk 56 optimal weight: 0.0980 chunk 163 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 419 optimal weight: 20.0000 chunk 180 optimal weight: 0.0010 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 ASN 3 219 HIS 3 422 GLN ** 3 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.274857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.228967 restraints weight = 78752.545| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 3.29 r_work: 0.4169 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44643 Z= 0.178 Angle : 0.714 27.299 61160 Z= 0.352 Chirality : 0.056 1.974 6013 Planarity : 0.005 0.065 7428 Dihedral : 17.620 178.663 10954 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 5.46 % Allowed : 26.31 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: -0.40 (0.11), residues: 5499 helix: 1.24 (0.12), residues: 1910 sheet: -0.51 (0.15), residues: 1156 loop : -1.37 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 59 TYR 0.039 0.002 TYR 3 970 PHE 0.036 0.002 PHE 3 788 TRP 0.016 0.002 TRP 3 903 HIS 0.006 0.001 HIS 1 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (44620) covalent geometry : angle 0.70452 / 0.35 (61146) hydrogen bonds : bond 0.04256 / 3.28 ( 2164) hydrogen bonds : angle 4.67511 / 5.00 ( 5923) metal coordination : bond 0.01012 / 0.65 ( 22) metal coordination : angle 7.74277 / 4.44 ( 14) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 294 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.2814 (OUTLIER) cc_final: 0.2386 (mtp) REVERT: 1 538 LEU cc_start: 0.8062 (tp) cc_final: 0.7739 (mp) REVERT: 1 623 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.5097 (t80) REVERT: 1 714 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: 1 775 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7677 (tmt-80) REVERT: 1 879 LEU cc_start: 0.8264 (mt) cc_final: 0.7953 (mm) REVERT: 1 910 MET cc_start: 0.4241 (mmp) cc_final: 0.3941 (mmp) REVERT: 1 966 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7752 (tp-100) REVERT: 1 1000 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6372 (tp) REVERT: 1 1156 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5125 (tp30) REVERT: 1 1287 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7574 (mp) REVERT: 2 529 LYS cc_start: 0.7816 (tttp) cc_final: 0.7243 (ptmt) REVERT: 3 66 MET cc_start: 0.8914 (mmm) cc_final: 0.8630 (tpt) REVERT: 3 69 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7205 (ttm170) REVERT: 3 219 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6951 (p90) REVERT: 3 273 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6323 (mtp180) REVERT: 3 278 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7261 (mt) REVERT: 3 331 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: 3 525 ARG cc_start: 0.4715 (OUTLIER) cc_final: 0.4366 (ptp-170) REVERT: 3 583 MET cc_start: -0.3092 (mmt) cc_final: -0.3539 (mtt) REVERT: 3 640 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7203 (pt) REVERT: 3 645 MET cc_start: -0.0620 (tmt) cc_final: -0.0910 (tpt) REVERT: 3 1001 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7863 (mm) REVERT: 3 1016 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.4251 (tpt170) REVERT: 3 1022 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7139 (mm) REVERT: E 158 GLU cc_start: 0.6027 (tm-30) cc_final: 0.5615 (tm-30) REVERT: E 198 TRP cc_start: 0.5450 (OUTLIER) cc_final: 0.4695 (p90) REVERT: E 235 VAL cc_start: 0.4902 (OUTLIER) cc_final: 0.4602 (t) REVERT: O 168 LYS cc_start: -0.2312 (OUTLIER) cc_final: -0.2658 (mmmt) REVERT: n 13 MET cc_start: -0.0634 (OUTLIER) cc_final: -0.1202 (tpp) REVERT: n 59 MET cc_start: -0.0755 (ttt) cc_final: -0.1273 (tpt) REVERT: l 41 MET cc_start: 0.1839 (ttp) cc_final: -0.0251 (tpt) REVERT: i 114 LEU cc_start: -0.0618 (OUTLIER) cc_final: -0.0896 (mt) REVERT: N 3 LYS cc_start: 0.0202 (OUTLIER) cc_final: -0.0396 (tmtt) REVERT: j 46 ILE cc_start: 0.0070 (OUTLIER) cc_final: -0.0151 (tp) outliers start: 167 outliers final: 90 residues processed: 435 average time/residue: 0.5902 time to fit residues: 333.2975 Evaluate side-chains 394 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 279 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 775 ARG Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 966 GLN Chi-restraints excluded: chain 1 residue 1000 ILE Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 40 LEU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 69 ARG Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 356 HIS Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 500 LEU Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1022 ILE Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 397 optimal weight: 0.9990 chunk 560 optimal weight: 3.9990 chunk 500 optimal weight: 9.9990 chunk 555 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 261 optimal weight: 50.0000 chunk 106 optimal weight: 0.5980 chunk 274 optimal weight: 20.0000 chunk 445 optimal weight: 30.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 526 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 749 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.274878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.225465 restraints weight = 77682.450| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 3.45 r_work: 0.4077 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 44643 Z= 0.307 Angle : 0.850 27.743 61160 Z= 0.426 Chirality : 0.062 1.991 6013 Planarity : 0.006 0.084 7428 Dihedral : 17.648 177.649 10954 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 6.47 % Allowed : 26.73 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: -0.64 (0.11), residues: 5499 helix: 1.02 (0.12), residues: 1898 sheet: -0.52 (0.15), residues: 1127 loop : -1.52 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 274 TYR 0.068 0.003 TYR 3 970 PHE 0.048 0.003 PHE 3 261 TRP 0.063 0.004 TRP E 198 HIS 0.065 0.002 HIS 3 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.31 (44620) covalent geometry : angle 0.83879 / 0.43 (61146) hydrogen bonds : bond 0.05203 / 3.96 ( 2164) hydrogen bonds : angle 4.96989 / 5.34 ( 5923) metal coordination : bond 0.01574 / 0.94 ( 22) metal coordination : angle 9.29987 / 5.36 ( 14) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 289 time to evaluate : 1.580 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: B 47 MET cc_start: 0.2979 (OUTLIER) cc_final: 0.2570 (mtp) REVERT: B 57 LYS cc_start: 0.5260 (pptt) cc_final: 0.5040 (pttt) REVERT: 1 538 LEU cc_start: 0.8081 (tp) cc_final: 0.7768 (mp) REVERT: 1 623 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5117 (t80) REVERT: 1 714 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: 1 775 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (tmt-80) REVERT: 1 799 ASP cc_start: 0.7627 (p0) cc_final: 0.7365 (p0) REVERT: 1 966 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7814 (tp-100) REVERT: 1 1156 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5193 (tp30) REVERT: 1 1193 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: 1 1287 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7608 (mp) REVERT: 2 502 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7943 (ptp-170) REVERT: 2 514 LYS cc_start: 0.4738 (OUTLIER) cc_final: 0.3896 (pmmt) REVERT: 2 529 LYS cc_start: 0.7879 (tttp) cc_final: 0.7196 (ptmt) REVERT: 2 586 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8983 (mt) REVERT: 3 69 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7262 (ttm170) REVERT: 3 146 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6165 (ptm-80) REVERT: 3 273 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6420 (mtp180) REVERT: 3 274 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6693 (mtt180) REVERT: 3 366 ASP cc_start: 0.6584 (m-30) cc_final: 0.6262 (m-30) REVERT: 3 400 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: 3 553 GLN cc_start: 0.4548 (OUTLIER) cc_final: 0.2740 (pm20) REVERT: 3 640 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7622 (pt) REVERT: 3 998 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.5854 (t-90) REVERT: 3 1001 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8069 (mm) REVERT: 3 1016 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4488 (tpt170) REVERT: 3 1022 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7471 (mm) REVERT: 3 1185 MET cc_start: 0.8836 (mtm) cc_final: 0.8543 (ptp) REVERT: C 399 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6101 (pt) REVERT: E 158 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: E 198 TRP cc_start: 0.5813 (OUTLIER) cc_final: 0.5063 (p90) REVERT: E 235 VAL cc_start: 0.5431 (OUTLIER) cc_final: 0.5209 (t) REVERT: O 168 LYS cc_start: -0.2458 (OUTLIER) cc_final: -0.2815 (mmmt) REVERT: m 27 MET cc_start: 0.0802 (ptp) cc_final: 0.0441 (ptp) REVERT: k 17 MET cc_start: 0.0360 (mmm) cc_final: -0.1340 (ptm) REVERT: n 13 MET cc_start: -0.0930 (OUTLIER) cc_final: -0.1452 (tpp) REVERT: n 59 MET cc_start: -0.0838 (ttt) cc_final: -0.1647 (mmt) REVERT: l 41 MET cc_start: 0.1960 (ttp) cc_final: -0.0184 (tpt) REVERT: i 114 LEU cc_start: -0.0269 (OUTLIER) cc_final: -0.0594 (mt) REVERT: N 3 LYS cc_start: 0.0228 (OUTLIER) cc_final: -0.0402 (tmtt) REVERT: j 46 ILE cc_start: 0.0138 (OUTLIER) cc_final: -0.0097 (tp) REVERT: 6 83 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.6162 (p0) outliers start: 198 outliers final: 110 residues processed: 455 average time/residue: 0.5570 time to fit residues: 329.4790 Evaluate side-chains 415 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 273 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 600 LEU Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 687 VAL Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 775 ARG Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 966 GLN Chi-restraints excluded: chain 1 residue 970 LEU Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1058 ILE Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1096 THR Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1103 VAL Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1161 MET Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1193 GLN Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 514 LYS Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 69 ARG Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 799 ILE Chi-restraints excluded: chain 3 residue 812 LYS Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 952 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1022 ILE Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1058 LEU Chi-restraints excluded: chain 3 residue 1091 VAL Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1200 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 22 LEU Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 552 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 377 optimal weight: 20.0000 chunk 403 optimal weight: 30.0000 chunk 152 optimal weight: 0.5980 chunk 417 optimal weight: 50.0000 chunk 402 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN 3 219 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 873 GLN ** 5 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.275927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.227776 restraints weight = 78499.090| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.54 r_work: 0.4135 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 44643 Z= 0.181 Angle : 0.725 27.352 61160 Z= 0.356 Chirality : 0.056 1.977 6013 Planarity : 0.005 0.072 7428 Dihedral : 17.539 178.563 10954 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 5.10 % Allowed : 27.94 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: -0.34 (0.11), residues: 5499 helix: 1.33 (0.13), residues: 1893 sheet: -0.42 (0.15), residues: 1124 loop : -1.35 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG m 73 TYR 0.039 0.002 TYR 3 970 PHE 0.045 0.002 PHE 3 261 TRP 0.022 0.002 TRP 3 903 HIS 0.017 0.001 HIS 3 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (44620) covalent geometry : angle 0.71476 / 0.36 (61146) hydrogen bonds : bond 0.04249 / 3.25 ( 2164) hydrogen bonds : angle 4.69315 / 5.03 ( 5923) metal coordination : bond 0.01023 / 0.64 ( 22) metal coordination : angle 7.93542 / 4.69 ( 14) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 298 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.2822 (OUTLIER) cc_final: 0.2472 (mtp) REVERT: B 57 LYS cc_start: 0.5094 (pptt) cc_final: 0.4844 (pptt) REVERT: 1 538 LEU cc_start: 0.8107 (tp) cc_final: 0.7777 (mp) REVERT: 1 623 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.5032 (t80) REVERT: 1 714 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: 1 775 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7644 (tmt-80) REVERT: 1 879 LEU cc_start: 0.8187 (mt) cc_final: 0.7901 (mm) REVERT: 1 1000 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5847 (tp) REVERT: 1 1156 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5126 (tp30) REVERT: 1 1193 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6361 (tt0) REVERT: 1 1287 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7543 (mp) REVERT: 2 529 LYS cc_start: 0.7833 (tttp) cc_final: 0.7132 (ptmm) REVERT: 3 69 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: 3 146 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5893 (ptm-80) REVERT: 3 222 ARG cc_start: 0.6829 (mtt90) cc_final: 0.6107 (mtm-85) REVERT: 3 273 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6317 (mtp180) REVERT: 3 400 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: 3 553 GLN cc_start: 0.4013 (OUTLIER) cc_final: 0.2236 (pm20) REVERT: 3 640 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7648 (pt) REVERT: 3 645 MET cc_start: 0.0438 (tmt) cc_final: 0.0026 (tpt) REVERT: 3 998 HIS cc_start: 0.6131 (OUTLIER) cc_final: 0.5626 (t-90) REVERT: 3 1001 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7905 (mm) REVERT: 3 1016 ARG cc_start: 0.4746 (OUTLIER) cc_final: 0.4375 (tpt170) REVERT: 3 1022 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7352 (mm) REVERT: 3 1185 MET cc_start: 0.8570 (mtm) cc_final: 0.8247 (ptp) REVERT: E 160 MET cc_start: 0.2849 (mmt) cc_final: 0.1768 (mpt) REVERT: E 198 TRP cc_start: 0.5725 (OUTLIER) cc_final: 0.4799 (p-90) REVERT: E 207 GLU cc_start: 0.5750 (mp0) cc_final: 0.4588 (mp0) REVERT: E 235 VAL cc_start: 0.5156 (OUTLIER) cc_final: 0.4937 (t) REVERT: O 168 LYS cc_start: -0.2344 (OUTLIER) cc_final: -0.2635 (mmmt) REVERT: m 27 MET cc_start: 0.0852 (ptp) cc_final: 0.0497 (ptp) REVERT: k 17 MET cc_start: -0.0090 (mmm) cc_final: -0.1734 (ptm) REVERT: n 13 MET cc_start: -0.1095 (OUTLIER) cc_final: -0.1642 (tpp) REVERT: n 59 MET cc_start: -0.0828 (ttt) cc_final: -0.1664 (mmt) REVERT: l 41 MET cc_start: 0.1887 (ttp) cc_final: -0.0208 (tpt) REVERT: i 114 LEU cc_start: -0.0296 (OUTLIER) cc_final: -0.0564 (mt) REVERT: N 3 LYS cc_start: 0.0135 (OUTLIER) cc_final: -0.0550 (tmtt) outliers start: 156 outliers final: 99 residues processed: 434 average time/residue: 0.5709 time to fit residues: 322.8300 Evaluate side-chains 414 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 291 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 775 ARG Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1000 ILE Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1103 VAL Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1193 GLN Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 69 ARG Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 356 HIS Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 952 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1022 ILE Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1058 LEU Chi-restraints excluded: chain 3 residue 1091 VAL Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 320 optimal weight: 50.0000 chunk 359 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 293 optimal weight: 30.0000 chunk 247 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 331 optimal weight: 0.4980 chunk 52 optimal weight: 0.2980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 626 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.274933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.228465 restraints weight = 77630.676| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 3.38 r_work: 0.4147 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 44643 Z= 0.192 Angle : 0.745 27.283 61160 Z= 0.365 Chirality : 0.057 1.978 6013 Planarity : 0.005 0.066 7428 Dihedral : 17.496 178.344 10953 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 5.13 % Allowed : 28.10 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.27 (0.11), residues: 5499 helix: 1.38 (0.12), residues: 1900 sheet: -0.38 (0.15), residues: 1131 loop : -1.32 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG m 73 TYR 0.045 0.002 TYR 3 970 PHE 0.042 0.002 PHE 3 788 TRP 0.020 0.002 TRP 3 903 HIS 0.007 0.001 HIS 11225 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (44620) covalent geometry : angle 0.73496 / 0.36 (61146) hydrogen bonds : bond 0.04316 / 3.29 ( 2164) hydrogen bonds : angle 4.66342 / 4.97 ( 5923) metal coordination : bond 0.00982 / 0.63 ( 22) metal coordination : angle 7.99656 / 4.73 ( 14) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 294 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 538 LEU cc_start: 0.8056 (tp) cc_final: 0.7745 (mp) REVERT: 1 623 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.5198 (t80) REVERT: 1 714 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6937 (tp30) REVERT: 1 879 LEU cc_start: 0.8150 (mt) cc_final: 0.7817 (mm) REVERT: 1 966 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7118 (mm-40) REVERT: 1 1156 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5099 (tp30) REVERT: 1 1193 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: 1 1287 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7601 (mp) REVERT: 2 514 LYS cc_start: 0.4115 (OUTLIER) cc_final: 0.3585 (pmmt) REVERT: 2 529 LYS cc_start: 0.7899 (tttp) cc_final: 0.7309 (ptpt) REVERT: 3 69 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7139 (ttm170) REVERT: 3 146 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5867 (ptm-80) REVERT: 3 366 ASP cc_start: 0.6289 (m-30) cc_final: 0.6077 (m-30) REVERT: 3 400 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: 3 553 GLN cc_start: 0.4455 (OUTLIER) cc_final: 0.2578 (pm20) REVERT: 3 592 LEU cc_start: 0.4908 (mt) cc_final: 0.4628 (pp) REVERT: 3 640 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7801 (pt) REVERT: 3 645 MET cc_start: 0.0331 (tmt) cc_final: -0.0045 (tpt) REVERT: 3 998 HIS cc_start: 0.6194 (OUTLIER) cc_final: 0.5509 (t-90) REVERT: 3 1001 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7910 (mm) REVERT: 3 1016 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.4411 (tpt170) REVERT: 3 1022 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7255 (mm) REVERT: 3 1105 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: 5 25 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5608 (t0) REVERT: E 198 TRP cc_start: 0.5850 (OUTLIER) cc_final: 0.5098 (p90) REVERT: E 207 GLU cc_start: 0.4751 (mp0) cc_final: 0.4428 (mp0) REVERT: E 235 VAL cc_start: 0.4719 (OUTLIER) cc_final: 0.4489 (t) REVERT: O 168 LYS cc_start: -0.2296 (OUTLIER) cc_final: -0.2607 (mmmt) REVERT: m 27 MET cc_start: 0.0883 (ptp) cc_final: 0.0534 (ptp) REVERT: m 72 ILE cc_start: 0.5400 (OUTLIER) cc_final: 0.5021 (tp) REVERT: n 13 MET cc_start: -0.1050 (OUTLIER) cc_final: -0.1556 (tpp) REVERT: n 59 MET cc_start: -0.1230 (ttt) cc_final: -0.1632 (mmt) REVERT: l 41 MET cc_start: 0.1932 (ttp) cc_final: -0.0136 (tpt) REVERT: N 3 LYS cc_start: -0.0051 (OUTLIER) cc_final: -0.0844 (tmtt) outliers start: 157 outliers final: 104 residues processed: 429 average time/residue: 0.5210 time to fit residues: 291.6518 Evaluate side-chains 413 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 286 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 761 TYR Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1193 GLN Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 514 LYS Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 69 ARG Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 123 VAL Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 356 HIS Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 665 LEU Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 812 LYS Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 952 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1022 ILE Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1058 LEU Chi-restraints excluded: chain 3 residue 1091 VAL Chi-restraints excluded: chain 3 residue 1105 GLN Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 5 residue 25 ASP Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 332 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 561 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 318 optimal weight: 40.0000 chunk 490 optimal weight: 0.0000 chunk 371 optimal weight: 10.0000 chunk 361 optimal weight: 50.0000 chunk 15 optimal weight: 50.0000 chunk 48 optimal weight: 0.0270 overall best weight: 0.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 422 GLN 3 626 GLN 3 707 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.276451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.228310 restraints weight = 78607.528| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 3.06 r_work: 0.4202 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44643 Z= 0.126 Angle : 0.689 26.912 61160 Z= 0.334 Chirality : 0.055 1.964 6013 Planarity : 0.005 0.134 7428 Dihedral : 17.418 177.035 10950 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 3.40 % Allowed : 29.93 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: -0.01 (0.12), residues: 5499 helix: 1.61 (0.13), residues: 1912 sheet: -0.27 (0.15), residues: 1145 loop : -1.18 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 12 TYR 0.020 0.001 TYR 3 970 PHE 0.036 0.002 PHE 3 261 TRP 0.022 0.002 TRP 3 460 HIS 0.007 0.001 HIS 3 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (44620) covalent geometry : angle 0.68168 / 0.33 (61146) hydrogen bonds : bond 0.03707 / 2.84 ( 2164) hydrogen bonds : angle 4.44150 / 4.71 ( 5923) metal coordination : bond 0.00675 / 0.49 ( 22) metal coordination : angle 6.83502 / 4.26 ( 14) Misc. bond : bond 0.00029 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 296 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 538 LEU cc_start: 0.7892 (tp) cc_final: 0.7601 (mp) REVERT: 1 620 MET cc_start: 0.6636 (mpp) cc_final: 0.6248 (pmm) REVERT: 1 623 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.4919 (t80) REVERT: 1 799 ASP cc_start: 0.7435 (p0) cc_final: 0.7180 (p0) REVERT: 1 874 LYS cc_start: 0.7205 (mttt) cc_final: 0.6977 (mtmt) REVERT: 1 966 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7069 (mm-40) REVERT: 1 1138 VAL cc_start: 0.6872 (t) cc_final: 0.6653 (m) REVERT: 2 514 LYS cc_start: 0.4118 (OUTLIER) cc_final: 0.3571 (pmmt) REVERT: 2 529 LYS cc_start: 0.7917 (tttp) cc_final: 0.7264 (ptpt) REVERT: 3 146 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.5830 (ptm-80) REVERT: 3 222 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6141 (mtm-85) REVERT: 3 316 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: 3 553 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.2602 (pm20) REVERT: 3 583 MET cc_start: -0.2535 (mmt) cc_final: -0.3075 (mtt) REVERT: 3 592 LEU cc_start: 0.5006 (mt) cc_final: 0.4595 (pp) REVERT: 3 640 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7747 (pt) REVERT: 3 645 MET cc_start: -0.0218 (tmt) cc_final: -0.0550 (tpt) REVERT: 3 998 HIS cc_start: 0.6399 (OUTLIER) cc_final: 0.5835 (t-90) REVERT: 3 1016 ARG cc_start: 0.4937 (OUTLIER) cc_final: 0.4381 (tpt170) REVERT: 3 1105 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: E 160 MET cc_start: 0.3034 (mmt) cc_final: 0.1681 (mpt) REVERT: E 198 TRP cc_start: 0.6000 (OUTLIER) cc_final: 0.5269 (p90) REVERT: E 235 VAL cc_start: 0.4581 (OUTLIER) cc_final: 0.4352 (t) REVERT: m 27 MET cc_start: 0.0801 (ptp) cc_final: 0.0454 (ptp) REVERT: n 13 MET cc_start: -0.0994 (OUTLIER) cc_final: -0.1578 (tpp) REVERT: n 59 MET cc_start: -0.1477 (ttt) cc_final: -0.1677 (mmt) REVERT: l 41 MET cc_start: 0.1995 (ttp) cc_final: -0.0049 (tpt) REVERT: l 78 MET cc_start: 0.2059 (ppp) cc_final: 0.0683 (pmt) REVERT: N 3 LYS cc_start: -0.0429 (OUTLIER) cc_final: -0.1077 (tmtt) outliers start: 104 outliers final: 69 residues processed: 383 average time/residue: 0.4184 time to fit residues: 209.1912 Evaluate side-chains 362 residues out of total 4942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 280 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 583 ILE Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 514 LYS Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 638 GLU Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1105 GLN Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 22 LEU Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 81 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 132 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 419 optimal weight: 7.9990 chunk 40 optimal weight: 50.0000 chunk 396 optimal weight: 40.0000 chunk 106 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 538 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 317 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 796 ASN l 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.276537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.230605 restraints weight = 79005.656| |-----------------------------------------------------------------------------| r_work (start): 0.4758 rms_B_bonded: 3.20 r_work: 0.4188 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44643 Z= 0.124 Angle : 0.679 26.849 61160 Z= 0.327 Chirality : 0.054 1.966 6013 Planarity : 0.005 0.062 7428 Dihedral : 17.356 178.459 10950 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 3.17 % Allowed : 30.33 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % 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: 0.15 (0.12), residues: 5499 helix: 1.73 (0.13), residues: 1921 sheet: -0.13 (0.15), residues: 1146 loop : -1.11 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG 1 852 TYR 0.022 0.001 TYR 1 587 PHE 0.032 0.002 PHE 3 702 TRP 0.021 0.002 TRP 3 460 HIS 0.007 0.001 HIS 11256 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (44620) covalent geometry : angle 0.67173 / 0.33 (61146) hydrogen bonds : bond 0.03599 / 2.75 ( 2164) hydrogen bonds : angle 4.33905 / 4.56 ( 5923) metal coordination : bond 0.00856 / 0.52 ( 22) metal coordination : angle 6.61171 / 4.10 ( 14) Misc. bond : bond 0.00024 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22456.39 seconds wall clock time: 380 minutes 35.83 seconds (22835.83 seconds total)