Starting phenix.real_space_refine on Mon Aug 10 10:29:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imk_60692/08_2026/9imk_60692.map" } resolution = 4.01 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= 0.033 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 16 6.06 5 P 176 5.49 5 S 312 5.16 5 C 27994 2.51 5 N 7600 2.21 5 O 9021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45119 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7473 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PTRANS': 30, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 925, 7447 Classifications: {'peptide': 925} Link IDs: {'PTRANS': 30, 'TRANS': 894} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7622 Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4500 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "P" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 853 Unusual residues: {'ATP': 1} Classifications: {'RNA': 39, 'undetermined': 1} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 2, 'rna3p': 36, None: 1} Not linked: pdbres="ATP P 1 " pdbres=" U P 2 " Chain: "R" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 977 Classifications: {'RNA': 46} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 21} Link IDs: {'rna2p': 1, 'rna3p': 44} Chain: "H" Number of atoms: 7473 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PTRANS': 30, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 925, 7447 Classifications: {'peptide': 925} Link IDs: {'PTRANS': 30, 'TRANS': 894} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7622 Chain: "I" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "K" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 4500 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "M" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "N" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "O" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 853 Unusual residues: {'ATP': 1} Classifications: {'RNA': 39, 'undetermined': 1} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 2, 'rna3p': 36, None: 1} Not linked: pdbres="ATP O 1 " pdbres=" U O 2 " Chain: "Q" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 977 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 22, 'rna3p_pyr': 21} Link IDs: {'rna2p': 2, 'rna3p': 43} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 40.234 105.566 45.108 1.00 38.17 S ATOM 2487 SG CYS A 306 40.190 108.518 42.663 1.00 24.21 S ATOM 2519 SG CYS A 310 37.592 108.395 45.490 1.00 48.77 S ATOM 3927 SG CYS A 487 57.459 94.208 47.714 1.00 35.25 S ATOM 5180 SG CYS A 645 58.041 96.720 44.943 1.00 47.35 S ATOM 5186 SG CYS A 646 54.698 94.858 45.179 1.00 49.77 S ATOM 10948 SG CYS E 16 76.421 61.680 95.123 1.00107.87 S ATOM 10963 SG CYS E 19 74.643 60.422 98.350 1.00104.26 S ATOM 10866 SG CYS E 5 82.472 67.626 103.839 1.00118.92 S ATOM 10887 SG CYS E 8 86.043 67.440 105.386 1.00112.81 S ATOM 11025 SG CYS E 26 85.613 68.197 101.641 1.00122.14 S ATOM 11042 SG CYS E 29 84.933 64.828 103.130 1.00115.45 S ATOM 11207 SG CYS E 50 78.453 66.908 77.118 1.00105.41 S ATOM 11237 SG CYS E 55 76.991 63.551 75.979 1.00107.16 S ATOM 11370 SG CYS E 72 80.703 64.374 75.235 1.00 94.87 S ATOM 15448 SG CYS F 16 66.034 51.890 52.012 1.00115.44 S ATOM 15463 SG CYS F 19 63.458 49.119 52.401 1.00117.66 S ATOM 15366 SG CYS F 5 68.334 48.971 63.333 1.00109.88 S ATOM 15387 SG CYS F 8 70.765 46.672 65.278 1.00110.93 S ATOM 15525 SG CYS F 26 72.156 49.562 63.170 1.00110.80 S ATOM 15542 SG CYS F 29 70.772 46.499 61.634 1.00106.71 S ATOM 15707 SG CYS F 50 75.077 66.701 44.629 1.00121.09 S ATOM 15737 SG CYS F 55 74.459 65.769 40.976 1.00120.47 S ATOM 15870 SG CYS F 72 77.960 65.293 42.466 1.00117.14 S ATOM 24996 SG CYS H 301 154.913 125.605 45.026 1.00 38.09 S ATOM 25037 SG CYS H 306 155.021 122.577 42.650 1.00 30.43 S ATOM 25069 SG CYS H 310 157.681 122.888 45.489 1.00 50.25 S ATOM 26477 SG CYS H 487 137.695 136.953 47.586 1.00 35.48 S ATOM 27730 SG CYS H 645 137.365 134.352 44.942 1.00 49.36 S ATOM 27736 SG CYS H 646 140.502 136.539 45.041 1.00 47.85 S ATOM 33498 SG CYS L 16 118.808 169.622 95.053 1.00108.24 S ATOM 33513 SG CYS L 19 120.498 170.814 98.369 1.00106.59 S ATOM 33416 SG CYS L 5 112.667 163.574 103.750 1.00119.81 S ATOM 33437 SG CYS L 8 109.078 163.800 105.333 1.00116.95 S ATOM 33575 SG CYS L 26 109.519 163.113 101.589 1.00116.77 S ATOM 33592 SG CYS L 29 110.273 166.433 103.080 1.00110.99 S ATOM 33757 SG CYS L 50 116.702 164.325 77.203 1.00104.31 S ATOM 33787 SG CYS L 55 118.211 167.575 75.881 1.00106.36 S ATOM 33920 SG CYS L 72 114.454 166.832 75.451 1.00 98.06 S ATOM 37998 SG CYS M 16 128.944 179.414 51.938 1.00119.38 S ATOM 38013 SG CYS M 19 131.697 182.060 52.443 1.00119.54 S ATOM 37916 SG CYS M 5 126.873 182.214 63.174 1.00110.14 S ATOM 37937 SG CYS M 8 124.505 184.570 65.256 1.00112.79 S ATOM 38075 SG CYS M 26 123.107 181.670 63.215 1.00108.40 S ATOM 38092 SG CYS M 29 124.393 184.786 61.655 1.00106.18 S ATOM 38257 SG CYS M 50 120.091 164.627 44.709 1.00122.40 S ATOM 38287 SG CYS M 55 120.746 165.312 41.011 1.00117.56 S ATOM 38420 SG CYS M 72 117.205 165.766 42.416 1.00117.64 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ALYS A 41 " occ=0.79 ... (7 atoms not shown) pdb=" NZ ALYS A 41 " occ=0.79 residue: pdb=" N AARG A 726 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG A 726 " occ=0.41 residue: pdb=" N AMET F 474 " occ=0.32 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.68 residue: pdb=" N ALYS H 41 " occ=0.83 ... (7 atoms not shown) pdb=" NZ ALYS H 41 " occ=0.83 residue: pdb=" N AARG H 726 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG H 726 " occ=0.49 residue: pdb=" N AMET M 474 " occ=0.29 ... (14 atoms not shown) pdb=" CE BMET M 474 " occ=0.71 Time building chain proxies: 13.63, per 1000 atoms: 0.30 Number of scatterers: 45119 At special positions: 0 Unit cell: (195.98, 232.06, 157.44, 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 16 29.99 S 312 16.00 P 176 15.00 O 9021 8.00 N 7600 7.00 C 27994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" ND1 HIS H 295 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 306 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 301 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 310 " pdb=" ZN H1002 " pdb="ZN ZN H1002 " - pdb=" ND1 HIS H 642 " pdb="ZN ZN H1002 " - pdb=" SG CYS H 487 " pdb="ZN ZN H1002 " - pdb=" SG CYS H 645 " pdb="ZN ZN H1002 " - pdb=" SG CYS H 646 " pdb=" ZN L 701 " pdb="ZN ZN L 701 " - pdb=" ND1 HIS L 39 " pdb="ZN ZN L 701 " - pdb=" NE2 HIS L 33 " pdb="ZN ZN L 701 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 701 " - pdb=" SG CYS L 16 " pdb=" ZN L 702 " pdb="ZN ZN L 702 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 702 " - pdb=" SG CYS L 26 " pdb="ZN ZN L 702 " - pdb=" SG CYS L 8 " pdb="ZN ZN L 702 " - pdb=" SG CYS L 5 " pdb=" ZN L 703 " pdb="ZN ZN L 703 " - pdb=" ND1 HIS L 75 " pdb="ZN ZN L 703 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 703 " - pdb=" SG CYS L 55 " pdb="ZN ZN L 703 " - pdb=" SG CYS L 72 " pdb=" ZN M 701 " pdb="ZN ZN M 701 " - pdb=" ND1 HIS M 39 " pdb="ZN ZN M 701 " - pdb=" NE2 HIS M 33 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 19 " pdb="ZN ZN M 701 " - pdb=" SG CYS M 16 " pdb=" ZN M 702 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 29 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 26 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 8 " pdb="ZN ZN M 702 " - pdb=" SG CYS M 5 " pdb=" ZN M 703 " pdb="ZN ZN M 703 " - pdb=" ND1 HIS M 75 " pdb="ZN ZN M 703 " - pdb=" SG CYS M 50 " pdb="ZN ZN M 703 " - pdb=" SG CYS M 55 " pdb="ZN ZN M 703 " - pdb=" SG CYS M 72 " Number of angles added : 56 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10132 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 61 sheets defined 44.1% alpha, 17.2% beta 68 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.552A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.579A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.509A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.945A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.063A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 5.372A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.941A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.673A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.699A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 459 removed outlier: 4.104A pdb=" N TYR A 453 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 457 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 459 " --> pdb=" O TYR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.956A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.656A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.684A pdb=" N LYS A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.619A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.989A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.881A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.619A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.507A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.184A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 31 through 55 removed outlier: 4.762A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 96 removed outlier: 4.119A pdb=" N MET B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.715A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.599A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.791A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.675A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.998A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.658A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.549A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 41 Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 54 through 80 removed outlier: 3.668A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.047A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.728A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.584A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.731A pdb=" N VAL E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.507A pdb=" N MET E 378 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 456 Processing helix chain 'E' and resid 489 through 503 Processing helix chain 'E' and resid 504 through 509 Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 533 through 537 Processing helix chain 'E' and resid 552 through 557 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 585 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.846A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.627A pdb=" N GLY F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.703A pdb=" N ALA F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.549A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 457 Processing helix chain 'F' and resid 490 through 503 Processing helix chain 'F' and resid 504 through 509 Processing helix chain 'F' and resid 515 through 527 Processing helix chain 'F' and resid 533 through 537 removed outlier: 3.566A pdb=" N GLN F 537 " --> pdb=" O VAL F 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 533 through 537' Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 585 Processing helix chain 'G' and resid 19 through 23 removed outlier: 4.268A pdb=" N CYS G 23 " --> pdb=" O GLN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'H' and resid 5 through 13 Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 76 through 88 removed outlier: 3.532A pdb=" N ILE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 133 removed outlier: 3.593A pdb=" N LEU H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 153 through 159 Processing helix chain 'H' and resid 170 through 177 removed outlier: 3.507A pdb=" N ASN H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 200 removed outlier: 3.937A pdb=" N VAL H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 248 Proline residue: H 243 - end of helix removed outlier: 4.095A pdb=" N THR H 246 " --> pdb=" O MET H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 removed outlier: 5.310A pdb=" N VAL H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP H 258 " --> pdb=" O SER H 255 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR H 259 " --> pdb=" O HIS H 256 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP H 260 " --> pdb=" O VAL H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 287 Processing helix chain 'H' and resid 297 through 301 removed outlier: 3.595A pdb=" N CYS H 301 " --> pdb=" O CYS H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 318 removed outlier: 4.018A pdb=" N PHE H 313 " --> pdb=" O HIS H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 326 removed outlier: 3.600A pdb=" N PHE H 326 " --> pdb=" O PRO H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 375 Processing helix chain 'H' and resid 377 through 385 removed outlier: 4.694A pdb=" N HIS H 381 " --> pdb=" O ASP H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 425 Processing helix chain 'H' and resid 448 through 459 removed outlier: 4.065A pdb=" N TYR H 453 " --> pdb=" O ILE H 450 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP H 454 " --> pdb=" O SER H 451 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG H 457 " --> pdb=" O ASP H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 477 Processing helix chain 'H' and resid 478 through 481 Processing helix chain 'H' and resid 511 through 519 removed outlier: 3.674A pdb=" N TYR H 515 " --> pdb=" O LYS H 511 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 531 Processing helix chain 'H' and resid 561 through 581 removed outlier: 5.111A pdb=" N PHE H 571 " --> pdb=" O THR H 567 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS H 574 " --> pdb=" O GLN H 570 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER H 578 " --> pdb=" O LYS H 574 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE H 579 " --> pdb=" O LEU H 575 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 581 " --> pdb=" O LYS H 577 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 606 Processing helix chain 'H' and resid 621 through 626 removed outlier: 3.741A pdb=" N MET H 626 " --> pdb=" O CYS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 640 Processing helix chain 'H' and resid 647 through 662 Processing helix chain 'H' and resid 687 through 710 removed outlier: 3.591A pdb=" N THR H 710 " --> pdb=" O ALA H 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 717 through 733 Processing helix chain 'H' and resid 738 through 752 Processing helix chain 'H' and resid 768 through 773 Processing helix chain 'H' and resid 778 through 791 removed outlier: 3.608A pdb=" N ASN H 791 " --> pdb=" O TYR H 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 795 through 799 removed outlier: 3.728A pdb=" N LYS H 798 " --> pdb=" O SER H 795 " (cutoff:3.500A) Processing helix chain 'H' and resid 804 through 808 Processing helix chain 'H' and resid 833 through 842 Processing helix chain 'H' and resid 847 through 851 Processing helix chain 'H' and resid 856 through 867 Processing helix chain 'H' and resid 868 through 872 removed outlier: 3.514A pdb=" N LYS H 871 " --> pdb=" O PRO H 868 " (cutoff:3.500A) Processing helix chain 'H' and resid 874 through 903 removed outlier: 4.284A pdb=" N ALA H 878 " --> pdb=" O ASN H 874 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE H 881 " --> pdb=" O TYR H 877 " (cutoff:3.500A) Processing helix chain 'H' and resid 910 through 916 removed outlier: 3.751A pdb=" N TRP H 916 " --> pdb=" O SER H 913 " (cutoff:3.500A) Processing helix chain 'H' and resid 917 through 923 removed outlier: 4.184A pdb=" N TYR H 921 " --> pdb=" O GLU H 917 " (cutoff:3.500A) Processing helix chain 'H' and resid 924 through 926 No H-bonds generated for 'chain 'H' and resid 924 through 926' Processing helix chain 'I' and resid 11 through 29 Processing helix chain 'I' and resid 31 through 55 removed outlier: 5.118A pdb=" N LYS I 37 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU I 38 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 96 removed outlier: 4.054A pdb=" N MET I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG I 96 " --> pdb=" O PHE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 109 removed outlier: 3.570A pdb=" N ASN I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.523A pdb=" N ASN I 140 " --> pdb=" O ASN I 136 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP I 143 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.606A pdb=" N ILE I 172 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 180 Processing helix chain 'J' and resid 3 through 20 Processing helix chain 'J' and resid 21 through 24 removed outlier: 3.641A pdb=" N SER J 24 " --> pdb=" O ARG J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 21 through 24' Processing helix chain 'J' and resid 25 through 42 Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.737A pdb=" N ALA J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 50 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL J 58 " --> pdb=" O SER J 54 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 71 Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.574A pdb=" N ALA K 13 " --> pdb=" O LEU K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 41 Processing helix chain 'K' and resid 43 through 48 removed outlier: 3.593A pdb=" N SER K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 80 removed outlier: 3.590A pdb=" N LYS K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 99 removed outlier: 4.018A pdb=" N GLN K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 113 removed outlier: 3.623A pdb=" N ILE K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 141 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 59 through 63 Processing helix chain 'L' and resid 103 through 112 Processing helix chain 'L' and resid 116 through 126 removed outlier: 3.798A pdb=" N TYR L 120 " --> pdb=" O ASN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 148 Processing helix chain 'L' and resid 259 through 264 removed outlier: 5.279A pdb=" N SER L 264 " --> pdb=" O GLU L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 273 Processing helix chain 'L' and resid 287 through 299 removed outlier: 3.655A pdb=" N ALA L 296 " --> pdb=" O ALA L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 325 removed outlier: 3.740A pdb=" N VAL L 314 " --> pdb=" O SER L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 328 No H-bonds generated for 'chain 'L' and resid 326 through 328' Processing helix chain 'L' and resid 361 through 363 No H-bonds generated for 'chain 'L' and resid 361 through 363' Processing helix chain 'L' and resid 375 through 379 Processing helix chain 'L' and resid 380 through 390 Processing helix chain 'L' and resid 418 through 422 Processing helix chain 'L' and resid 423 through 432 Processing helix chain 'L' and resid 445 through 456 Processing helix chain 'L' and resid 489 through 503 Processing helix chain 'L' and resid 504 through 509 Processing helix chain 'L' and resid 515 through 526 Processing helix chain 'L' and resid 533 through 537 removed outlier: 3.508A pdb=" N GLN L 537 " --> pdb=" O VAL L 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 533 through 537' Processing helix chain 'L' and resid 552 through 557 Processing helix chain 'L' and resid 557 through 566 Processing helix chain 'L' and resid 578 through 585 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 103 through 112 Processing helix chain 'M' and resid 116 through 126 removed outlier: 3.901A pdb=" N TYR M 120 " --> pdb=" O ASN M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 148 Processing helix chain 'M' and resid 262 through 264 No H-bonds generated for 'chain 'M' and resid 262 through 264' Processing helix chain 'M' and resid 265 through 273 removed outlier: 3.540A pdb=" N GLY M 273 " --> pdb=" O TYR M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 299 removed outlier: 3.802A pdb=" N ALA M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 325 removed outlier: 3.553A pdb=" N VAL M 314 " --> pdb=" O SER M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 379 Processing helix chain 'M' and resid 380 through 390 Processing helix chain 'M' and resid 418 through 422 removed outlier: 3.544A pdb=" N PHE M 422 " --> pdb=" O PRO M 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 423 through 432 Processing helix chain 'M' and resid 445 through 457 Processing helix chain 'M' and resid 490 through 503 Processing helix chain 'M' and resid 504 through 509 Processing helix chain 'M' and resid 515 through 526 Processing helix chain 'M' and resid 533 through 537 removed outlier: 3.542A pdb=" N GLN M 537 " --> pdb=" O VAL M 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 533 through 537' Processing helix chain 'M' and resid 557 through 566 Processing helix chain 'M' and resid 578 through 585 Processing helix chain 'N' and resid 95 through 110 removed outlier: 3.546A pdb=" N ARG N 99 " --> pdb=" O ASN N 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 6.099A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 6.099A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.583A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.537A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 115 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.677A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.572A pdb=" N ASN A 414 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.010A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.010A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'E' and resid 69 through 71 removed outlier: 3.925A pdb=" N PHE E 81 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 159 removed outlier: 6.911A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 347 through 348 removed outlier: 3.984A pdb=" N LYS E 347 " --> pdb=" O CYS E 330 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N THR E 367 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N HIS E 395 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP E 369 " --> pdb=" O HIS E 395 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL E 397 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 440 through 441 Processing sheet with id=AC1, first strand: chain 'E' and resid 530 through 532 removed outlier: 7.992A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS E 471 " --> pdb=" O THR E 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 159 removed outlier: 7.116A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL F 157 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU F 162 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 152 " --> pdb=" O PHE F 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 347 through 348 removed outlier: 3.928A pdb=" N LYS F 347 " --> pdb=" O CYS F 330 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N MET F 436 " --> pdb=" O TYR F 277 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR F 279 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 440 through 441 Processing sheet with id=AD1, first strand: chain 'F' and resid 530 through 532 removed outlier: 8.262A pdb=" N ASP F 542 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE F 572 " --> pdb=" O ASP F 542 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL F 544 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N CYS F 574 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE F 546 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N MET F 576 " --> pdb=" O PHE F 546 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N AMET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS F 471 " --> pdb=" O THR F 588 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 480 through 482 Processing sheet with id=AD3, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.905A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N SER G 13 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN G 33 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL G 41 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR G 35 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 31 through 38 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 4.216A pdb=" N GLU H 58 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.564A pdb=" N TYR H 69 " --> pdb=" O ARG H 118 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 223 through 224 removed outlier: 7.572A pdb=" N ILE H 201 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 352 through 355 removed outlier: 5.420A pdb=" N SER H 343 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG H 331 " --> pdb=" O SER H 343 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 334 through 335 Processing sheet with id=AE1, first strand: chain 'H' and resid 556 through 559 removed outlier: 3.573A pdb=" N MET H 668 " --> pdb=" O THR H 540 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET H 542 " --> pdb=" O MET H 668 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU H 673 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL H 398 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU H 388 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 158 " --> pdb=" O THR I 187 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU I 189 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE I 156 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 414 through 415 Processing sheet with id=AE3, first strand: chain 'H' and resid 753 through 758 removed outlier: 4.705A pdb=" N ALA H 762 " --> pdb=" O TRP H 617 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP H 617 " --> pdb=" O ALA H 762 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 816 through 821 Processing sheet with id=AE5, first strand: chain 'K' and resid 127 through 132 removed outlier: 3.596A pdb=" N GLN K 158 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU K 189 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE K 156 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR K 146 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 127 through 132 removed outlier: 3.596A pdb=" N GLN K 158 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU K 189 " --> pdb=" O ILE K 156 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE K 156 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL K 159 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'L' and resid 15 through 16 Processing sheet with id=AE9, first strand: chain 'L' and resid 64 through 66 Processing sheet with id=AF1, first strand: chain 'L' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'L' and resid 152 through 159 removed outlier: 6.939A pdb=" N HIS L 164 " --> pdb=" O ARG L 155 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL L 157 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLU L 162 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN L 194 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG L 186 " --> pdb=" O GLN L 194 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY L 196 " --> pdb=" O GLY L 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 152 " --> pdb=" O PHE L 225 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 347 through 348 removed outlier: 3.928A pdb=" N LYS L 347 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER L 331 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR L 359 " --> pdb=" O SER L 331 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR L 367 " --> pdb=" O ALA L 393 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N HIS L 395 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP L 369 " --> pdb=" O HIS L 395 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL L 397 " --> pdb=" O ASP L 369 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL L 371 " --> pdb=" O VAL L 397 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE L 399 " --> pdb=" O VAL L 371 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE L 373 " --> pdb=" O ILE L 399 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N MET L 436 " --> pdb=" O TYR L 277 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR L 279 " --> pdb=" O MET L 436 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 440 through 441 Processing sheet with id=AF5, first strand: chain 'L' and resid 530 through 532 removed outlier: 8.349A pdb=" N ASP L 542 " --> pdb=" O VAL L 570 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE L 572 " --> pdb=" O ASP L 542 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL L 544 " --> pdb=" O ILE L 572 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N CYS L 574 " --> pdb=" O VAL L 544 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE L 546 " --> pdb=" O CYS L 574 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N MET L 576 " --> pdb=" O PHE L 546 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS L 471 " --> pdb=" O THR L 588 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 481 through 482 Processing sheet with id=AF7, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AF8, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AF9, first strand: chain 'M' and resid 63 through 66 Processing sheet with id=AG1, first strand: chain 'M' and resid 84 through 85 Processing sheet with id=AG2, first strand: chain 'M' and resid 152 through 159 removed outlier: 7.072A pdb=" N HIS M 164 " --> pdb=" O ARG M 155 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL M 157 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU M 162 " --> pdb=" O VAL M 157 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN M 194 " --> pdb=" O ARG M 186 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG M 186 " --> pdb=" O GLN M 194 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY M 196 " --> pdb=" O GLY M 184 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA M 152 " --> pdb=" O PHE M 225 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 347 through 348 removed outlier: 3.924A pdb=" N LYS M 347 " --> pdb=" O CYS M 330 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER M 331 " --> pdb=" O PHE M 357 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR M 359 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE M 304 " --> pdb=" O VAL M 356 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N CYS M 358 " --> pdb=" O ILE M 304 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR M 306 " --> pdb=" O CYS M 358 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N THR M 367 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N HIS M 395 " --> pdb=" O THR M 367 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP M 369 " --> pdb=" O HIS M 395 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL M 397 " --> pdb=" O ASP M 369 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL M 371 " --> pdb=" O VAL M 397 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE M 399 " --> pdb=" O VAL M 371 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE M 373 " --> pdb=" O ILE M 399 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 440 through 441 Processing sheet with id=AG5, first strand: chain 'M' and resid 530 through 532 removed outlier: 8.280A pdb=" N ASP M 542 " --> pdb=" O VAL M 570 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE M 572 " --> pdb=" O ASP M 542 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL M 544 " --> pdb=" O ILE M 572 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N CYS M 574 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE M 546 " --> pdb=" O CYS M 574 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET M 576 " --> pdb=" O PHE M 546 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE M 472 " --> pdb=" O CYS M 574 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET M 576 " --> pdb=" O PHE M 472 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N AMET M 474 " --> pdb=" O MET M 576 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS M 471 " --> pdb=" O THR M 588 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 480 through 482 Processing sheet with id=AG7, first strand: chain 'N' and resid 64 through 68 removed outlier: 3.869A pdb=" N ALA N 15 " --> pdb=" O ARG N 55 " (cutoff:3.500A) removed outlier: 12.251A pdb=" N SER N 13 " --> pdb=" O PRO N 57 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 29 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU N 44 " --> pdb=" O LEU N 29 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR N 31 " --> pdb=" O LEU N 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR N 35 " --> pdb=" O GLY N 38 " (cutoff:3.500A) 1895 hydrogen bonds defined for protein. 5175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 160 hydrogen bonds 312 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 13.38 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7315 1.32 - 1.45: 13379 1.45 - 1.57: 24941 1.57 - 1.70: 349 1.70 - 1.82: 442 Bond restraints: 46426 Sorted by residual: bond pdb=" P U P 2 " pdb=" OP1 U P 2 " ideal model delta sigma weight residual 1.485 1.329 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C1' G Q 41 " pdb=" N9 G Q 41 " ideal model delta sigma weight residual 1.483 1.377 0.106 1.50e-02 4.44e+03 5.01e+01 bond pdb=" C1' G R 41 " pdb=" N9 G R 41 " ideal model delta sigma weight residual 1.483 1.377 0.106 1.50e-02 4.44e+03 4.97e+01 bond pdb=" C1' G R 39 " pdb=" N9 G R 39 " ideal model delta sigma weight residual 1.483 1.382 0.101 1.50e-02 4.44e+03 4.53e+01 bond pdb=" C1' G Q 39 " pdb=" N9 G Q 39 " ideal model delta sigma weight residual 1.483 1.383 0.100 1.50e-02 4.44e+03 4.47e+01 ... (remaining 46421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.27: 63852 6.27 - 12.54: 57 12.54 - 18.81: 1 18.81 - 25.08: 3 25.08 - 31.35: 1 Bond angle restraints: 63914 Sorted by residual: angle pdb=" C PHE H 504 " pdb=" N PRO H 505 " pdb=" CA PRO H 505 " ideal model delta sigma weight residual 119.84 88.49 31.35 1.25e+00 6.40e-01 6.29e+02 angle pdb=" C PHE A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta sigma weight residual 120.12 110.36 9.76 1.11e+00 8.12e-01 7.74e+01 angle pdb=" OP1 U P 2 " pdb=" P U P 2 " pdb=" O5' U P 2 " ideal model delta sigma weight residual 108.00 85.87 22.13 3.00e+00 1.11e-01 5.44e+01 angle pdb=" OP1 U O 2 " pdb=" P U O 2 " pdb=" O5' U O 2 " ideal model delta sigma weight residual 108.00 87.44 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" N LYS D 40 " pdb=" CA LYS D 40 " pdb=" C LYS D 40 " ideal model delta sigma weight residual 112.89 104.56 8.33 1.24e+00 6.50e-01 4.52e+01 ... (remaining 63909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 27213 35.41 - 70.82: 704 70.82 - 106.23: 72 106.23 - 141.64: 3 141.64 - 177.05: 6 Dihedral angle restraints: 27998 sinusoidal: 12292 harmonic: 15706 Sorted by residual: dihedral pdb=" O4' U O 3 " pdb=" C1' U O 3 " pdb=" N1 U O 3 " pdb=" C2 U O 3 " ideal model delta sinusoidal sigma weight residual 232.00 79.21 152.79 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" CA TRP I 182 " pdb=" C TRP I 182 " pdb=" N PRO I 183 " pdb=" CA PRO I 183 " ideal model delta harmonic sigma weight residual 180.00 140.74 39.26 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 141.39 38.61 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 27995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 7371 0.136 - 0.273: 86 0.273 - 0.409: 0 0.409 - 0.546: 0 0.546 - 0.682: 1 Chirality restraints: 7458 Sorted by residual: chirality pdb=" CA PHE A 504 " pdb=" N PHE A 504 " pdb=" C PHE A 504 " pdb=" CB PHE A 504 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE H 504 " pdb=" N PHE H 504 " pdb=" C PHE H 504 " pdb=" CB PHE H 504 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' C R 15 " pdb=" C4' C R 15 " pdb=" O3' C R 15 " pdb=" C2' C R 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 7455 not shown) Planarity restraints: 7530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 70 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO N 71 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO N 71 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO N 71 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " 0.031 2.00e-02 2.50e+03 3.57e-02 2.23e+01 pdb=" CG PHE I 15 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 504 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO H 505 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO H 505 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 505 " 0.080 5.00e-02 4.00e+02 ... (remaining 7527 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 380 2.55 - 3.14: 36420 3.14 - 3.72: 75479 3.72 - 4.31: 103106 4.31 - 4.90: 162758 Nonbonded interactions: 378143 Sorted by model distance: nonbonded pdb=" O PHE H 504 " pdb=" CA PRO H 505 " model vdw 1.962 2.776 nonbonded pdb=" O ILE A 864 " pdb=" OH TYR A 925 " model vdw 2.079 3.040 nonbonded pdb=" O GLN N 49 " pdb=" OH TYR N 89 " model vdw 2.086 3.040 nonbonded pdb=" OD2 ASP I 50 " pdb=" O2' C O 21 " model vdw 2.144 3.040 nonbonded pdb=" O ASN A 138 " pdb=" ND2 ASN A 138 " model vdw 2.149 3.120 ... (remaining 378138 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 40 or resid 42 through 72 or resid 74 through 72 \ 5 or resid 727 through 1002)) selection = (chain 'H' and (resid 4 through 40 or resid 42 through 72 or resid 74 through 72 \ 5 or resid 727 through 1002)) } ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) selection = (chain 'I' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'K' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'L' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'M' and (resid 2 through 473 or resid 475 through 703)) } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.740 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 60.010 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.170 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 : 0.004 0.156 46492 Z= 0.227 Angle : 0.768 31.346 63970 Z= 0.474 Chirality : 0.048 0.682 7458 Planarity : 0.005 0.119 7530 Dihedral : 15.276 177.053 17866 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 0.26 % Favored : 99.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.81 (0.11), residues: 5276 helix: 0.15 (0.11), residues: 2042 sheet: -0.39 (0.19), residues: 680 loop : -1.09 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 155 TYR 0.030 0.002 TYR L 93 PHE 0.083 0.002 PHE I 15 TRP 0.013 0.002 TRP K 182 HIS 0.014 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.23 (46426) covalent geometry : angle 0.76347 / 0.47 (63914) hydrogen bonds : bond 0.16219 / 10.74 ( 2029) hydrogen bonds : angle 6.55770 / 4.55 ( 5487) metal coordination : bond 0.01213 / 0.83 ( 64) metal coordination : angle 2.90089 / 2.09 ( 56) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 392 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8151 (p0) cc_final: 0.7777 (p0) REVERT: A 855 MET cc_start: 0.5472 (ptt) cc_final: 0.5153 (ptm) REVERT: A 899 MET cc_start: 0.8112 (ppp) cc_final: 0.7773 (ppp) REVERT: F 436 MET cc_start: 0.3835 (pmm) cc_final: 0.3604 (pmm) REVERT: G 75 PHE cc_start: 0.7271 (p90) cc_final: 0.6849 (p90) REVERT: H 855 MET cc_start: 0.6054 (ptt) cc_final: 0.4249 (ptp) REVERT: H 899 MET cc_start: 0.7914 (ppp) cc_final: 0.7492 (ppp) REVERT: K 70 MET cc_start: 0.7315 (ppp) cc_final: 0.6806 (ppp) outliers start: 5 outliers final: 1 residues processed: 397 average time/residue: 0.2712 time to fit residues: 181.0681 Evaluate side-chains 270 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 30.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 39 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS A 898 HIS B 109 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN E 62 GLN E 516 ASN F 46 ASN F 51 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 541 GLN ** H 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 ASN L 516 ASN M 51 ASN M 88 GLN M 124 ASN M 164 HIS M 194 GLN N 98 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.120833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.102264 restraints weight = 322261.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099296 restraints weight = 321678.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.097918 restraints weight = 244127.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.098163 restraints weight = 234003.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097949 restraints weight = 161880.669| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 46492 Z= 0.372 Angle : 0.866 14.234 63970 Z= 0.453 Chirality : 0.052 0.387 7458 Planarity : 0.006 0.079 7530 Dihedral : 15.304 174.838 8408 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.24 (0.11), residues: 5276 helix: -0.27 (0.11), residues: 2072 sheet: -0.91 (0.18), residues: 762 loop : -1.19 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 105 TYR 0.040 0.003 TYR H 38 PHE 0.046 0.003 PHE H 753 TRP 0.019 0.003 TRP H 290 HIS 0.012 0.002 HIS H 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.37 (46426) covalent geometry : angle 0.85530 / 0.45 (63914) hydrogen bonds : bond 0.06608 / 4.34 ( 2029) hydrogen bonds : angle 5.72292 / 3.97 ( 5487) metal coordination : bond 0.04097 / 2.74 ( 64) metal coordination : angle 4.75424 / 3.20 ( 56) Misc. bond : bond 0.00179 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 341 time to evaluate : 1.721 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: A 420 TYR cc_start: 0.6917 (t80) cc_final: 0.6687 (t80) REVERT: A 500 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8111 (mmmm) REVERT: A 665 GLU cc_start: 0.8389 (pm20) cc_final: 0.7476 (pm20) REVERT: A 899 MET cc_start: 0.8323 (ppp) cc_final: 0.8004 (ppp) REVERT: B 72 LYS cc_start: 0.9251 (pttp) cc_final: 0.8816 (pptt) REVERT: B 75 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.8079 (ttp-110) REVERT: C 5 ASP cc_start: 0.7629 (m-30) cc_final: 0.7208 (m-30) REVERT: D 48 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: H 420 TYR cc_start: 0.6807 (t80) cc_final: 0.6312 (t80) REVERT: H 601 MET cc_start: 0.8411 (mtt) cc_final: 0.8109 (mtp) REVERT: H 899 MET cc_start: 0.8242 (ppp) cc_final: 0.7863 (ppp) REVERT: I 87 MET cc_start: 0.9059 (ttm) cc_final: 0.8816 (ttp) REVERT: J 5 ASP cc_start: 0.7652 (m-30) cc_final: 0.7069 (m-30) REVERT: N 75 PHE cc_start: 0.7347 (p90) cc_final: 0.7024 (p90) outliers start: 4 outliers final: 0 residues processed: 344 average time/residue: 0.2716 time to fit residues: 155.7064 Evaluate side-chains 240 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 281 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 420 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN E 124 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN J 34 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 ASN M 51 ASN M 124 ASN M 164 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.122393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.101665 restraints weight = 280287.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.098623 restraints weight = 295141.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095605 restraints weight = 206731.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.096080 restraints weight = 181332.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.095812 restraints weight = 130046.488| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 46492 Z= 0.198 Angle : 0.659 11.967 63970 Z= 0.345 Chirality : 0.044 0.372 7458 Planarity : 0.005 0.072 7530 Dihedral : 15.287 174.027 8408 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.92 (0.11), residues: 5276 helix: 0.03 (0.11), residues: 2072 sheet: -0.73 (0.19), residues: 744 loop : -1.04 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 75 TYR 0.027 0.002 TYR A 32 PHE 0.063 0.002 PHE B 49 TRP 0.013 0.002 TRP D 182 HIS 0.010 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (46426) covalent geometry : angle 0.64727 / 0.34 (63914) hydrogen bonds : bond 0.05204 / 3.46 ( 2029) hydrogen bonds : angle 5.27600 / 3.66 ( 5487) metal coordination : bond 0.02439 / 1.65 ( 64) metal coordination : angle 4.15884 / 3.00 ( 56) Misc. bond : bond 0.00113 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 337 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.6765 (t80) cc_final: 0.6541 (t80) REVERT: A 899 MET cc_start: 0.8536 (ppp) cc_final: 0.8226 (ppp) REVERT: B 62 MET cc_start: 0.8014 (ppp) cc_final: 0.7736 (ptm) REVERT: C 5 ASP cc_start: 0.7456 (m-30) cc_final: 0.6913 (m-30) REVERT: E 124 ASN cc_start: 0.0141 (OUTLIER) cc_final: -0.0071 (m-40) REVERT: G 12 MET cc_start: 0.7512 (ttt) cc_final: 0.7201 (ttm) REVERT: H 601 MET cc_start: 0.8370 (mtt) cc_final: 0.8055 (mtp) REVERT: H 899 MET cc_start: 0.8391 (ppp) cc_final: 0.8123 (ppp) REVERT: I 87 MET cc_start: 0.8896 (ttm) cc_final: 0.8693 (ttp) REVERT: K 67 MET cc_start: 0.7882 (ttt) cc_final: 0.7652 (ttt) outliers start: 4 outliers final: 1 residues processed: 341 average time/residue: 0.2508 time to fit residues: 144.4729 Evaluate side-chains 237 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 492 optimal weight: 1.9990 chunk 354 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 422 optimal weight: 0.0020 chunk 283 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 403 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 365 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS G 1 ASN H 541 GLN ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN L 124 ASN M 46 ASN M 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.121674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.101230 restraints weight = 347272.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.098936 restraints weight = 327022.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096013 restraints weight = 208958.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.096510 restraints weight = 208590.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.095985 restraints weight = 149704.449| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 46492 Z= 0.200 Angle : 0.651 12.313 63970 Z= 0.340 Chirality : 0.044 0.361 7458 Planarity : 0.005 0.141 7530 Dihedral : 15.157 173.309 8408 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.89 (0.11), residues: 5276 helix: 0.12 (0.11), residues: 2092 sheet: -0.77 (0.19), residues: 744 loop : -1.09 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 111 TYR 0.024 0.002 TYR A 32 PHE 0.036 0.002 PHE B 15 TRP 0.020 0.002 TRP D 182 HIS 0.009 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (46426) covalent geometry : angle 0.63986 / 0.34 (63914) hydrogen bonds : bond 0.04894 / 3.25 ( 2029) hydrogen bonds : angle 5.13294 / 3.57 ( 5487) metal coordination : bond 0.02373 / 1.60 ( 64) metal coordination : angle 4.13960 / 2.97 ( 56) Misc. bond : bond 0.00107 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.7556 (tpp) cc_final: 0.7271 (tpp) REVERT: A 542 MET cc_start: 0.8689 (tpp) cc_final: 0.8423 (tpt) REVERT: A 601 MET cc_start: 0.8128 (mtt) cc_final: 0.7914 (mtp) REVERT: A 899 MET cc_start: 0.8555 (ppp) cc_final: 0.8300 (ppp) REVERT: B 62 MET cc_start: 0.8066 (ppp) cc_final: 0.7782 (ptm) REVERT: B 72 LYS cc_start: 0.9509 (pptt) cc_final: 0.9301 (pptt) REVERT: D 48 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: G 12 MET cc_start: 0.7578 (ttt) cc_final: 0.7265 (ttm) REVERT: H 899 MET cc_start: 0.8385 (ppp) cc_final: 0.8109 (ppp) REVERT: H 924 MET cc_start: 0.7878 (mmm) cc_final: 0.7605 (mmm) REVERT: K 67 MET cc_start: 0.7847 (ttt) cc_final: 0.7357 (ptm) REVERT: L 233 MET cc_start: 0.7533 (ppp) cc_final: 0.7324 (ppp) outliers start: 3 outliers final: 0 residues processed: 330 average time/residue: 0.2403 time to fit residues: 133.8086 Evaluate side-chains 224 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 343 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 523 optimal weight: 30.0000 chunk 434 optimal weight: 4.9990 chunk 495 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 306 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.122515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.101686 restraints weight = 363396.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098012 restraints weight = 335708.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.095583 restraints weight = 201425.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.095407 restraints weight = 193758.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.095219 restraints weight = 141834.761| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 46492 Z= 0.145 Angle : 0.602 10.991 63970 Z= 0.312 Chirality : 0.042 0.359 7458 Planarity : 0.004 0.110 7530 Dihedral : 15.075 172.471 8408 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.71 (0.11), residues: 5276 helix: 0.28 (0.11), residues: 2092 sheet: -0.62 (0.19), residues: 716 loop : -1.01 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.021 0.001 TYR A 32 PHE 0.041 0.002 PHE B 15 TRP 0.016 0.001 TRP D 182 HIS 0.011 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (46426) covalent geometry : angle 0.59237 / 0.31 (63914) hydrogen bonds : bond 0.04405 / 2.94 ( 2029) hydrogen bonds : angle 4.94678 / 3.45 ( 5487) metal coordination : bond 0.01882 / 1.29 ( 64) metal coordination : angle 3.69892 / 2.66 ( 56) Misc. bond : bond 0.00092 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.524 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: A 380 MET cc_start: 0.7367 (tpp) cc_final: 0.7138 (tpp) REVERT: A 665 GLU cc_start: 0.8024 (pm20) cc_final: 0.7281 (pm20) REVERT: A 899 MET cc_start: 0.8687 (ppp) cc_final: 0.8473 (ppp) REVERT: E 233 MET cc_start: 0.7615 (ppp) cc_final: 0.7386 (ppp) REVERT: G 12 MET cc_start: 0.7792 (ttt) cc_final: 0.7477 (ttm) REVERT: H 601 MET cc_start: 0.8276 (mtt) cc_final: 0.8012 (mtp) REVERT: H 899 MET cc_start: 0.8528 (ppp) cc_final: 0.8260 (ppp) REVERT: K 67 MET cc_start: 0.8104 (ttt) cc_final: 0.7784 (ptm) REVERT: L 233 MET cc_start: 0.7849 (ppp) cc_final: 0.7624 (ppp) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2143 time to fit residues: 119.2090 Evaluate side-chains 227 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 415 optimal weight: 8.9990 chunk 187 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 305 optimal weight: 0.0470 chunk 256 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN N 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.122766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.101956 restraints weight = 368758.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.099873 restraints weight = 333598.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.097577 restraints weight = 188847.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.097952 restraints weight = 185098.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.097702 restraints weight = 132086.613| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 46492 Z= 0.131 Angle : 0.591 11.897 63970 Z= 0.306 Chirality : 0.042 0.351 7458 Planarity : 0.004 0.140 7530 Dihedral : 14.971 171.648 8408 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 5276 helix: 0.35 (0.11), residues: 2084 sheet: -0.63 (0.19), residues: 750 loop : -0.97 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 74 TYR 0.026 0.001 TYR A 903 PHE 0.055 0.002 PHE D 15 TRP 0.015 0.001 TRP D 182 HIS 0.011 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (46426) covalent geometry : angle 0.58197 / 0.31 (63914) hydrogen bonds : bond 0.04221 / 2.83 ( 2029) hydrogen bonds : angle 4.83344 / 3.37 ( 5487) metal coordination : bond 0.01677 / 1.19 ( 64) metal coordination : angle 3.50901 / 2.62 ( 56) Misc. bond : bond 0.00080 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.346 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: A 380 MET cc_start: 0.7387 (tpp) cc_final: 0.7084 (tpp) REVERT: A 601 MET cc_start: 0.7991 (mtt) cc_final: 0.7787 (mtp) REVERT: H 542 MET cc_start: 0.8364 (tpp) cc_final: 0.8154 (mmt) REVERT: H 601 MET cc_start: 0.8121 (mtt) cc_final: 0.7869 (mtp) REVERT: K 67 MET cc_start: 0.7893 (ttt) cc_final: 0.7457 (ptm) REVERT: L 233 MET cc_start: 0.7540 (ppp) cc_final: 0.7333 (ppp) REVERT: N 75 PHE cc_start: 0.7193 (p90) cc_final: 0.6770 (p90) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2184 time to fit residues: 118.7515 Evaluate side-chains 222 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 379 optimal weight: 0.0870 chunk 463 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 414 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 482 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 492 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 213 optimal weight: 50.0000 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS F 275 GLN ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.123031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.102741 restraints weight = 297159.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.100137 restraints weight = 315981.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.097934 restraints weight = 199153.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.098020 restraints weight = 190613.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.097930 restraints weight = 137679.699| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 46492 Z= 0.120 Angle : 0.578 10.567 63970 Z= 0.298 Chirality : 0.041 0.340 7458 Planarity : 0.004 0.101 7530 Dihedral : 14.832 170.960 8408 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 0.02 % Allowed : 0.70 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.56 (0.11), residues: 5276 helix: 0.44 (0.11), residues: 2086 sheet: -0.59 (0.19), residues: 750 loop : -0.94 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.028 0.001 TYR K 71 PHE 0.072 0.002 PHE B 49 TRP 0.016 0.001 TRP H 509 HIS 0.011 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (46426) covalent geometry : angle 0.57005 / 0.30 (63914) hydrogen bonds : bond 0.03943 / 2.63 ( 2029) hydrogen bonds : angle 4.69954 / 3.28 ( 5487) metal coordination : bond 0.01594 / 1.17 ( 64) metal coordination : angle 3.32487 / 2.46 ( 56) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.044 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: A 899 MET cc_start: 0.8590 (ppp) cc_final: 0.8356 (ppp) REVERT: B 67 MET cc_start: 0.7827 (tpp) cc_final: 0.7604 (tpp) REVERT: B 87 MET cc_start: 0.8076 (ttt) cc_final: 0.7649 (ttt) REVERT: D 55 MET cc_start: 0.8716 (pmm) cc_final: 0.8498 (pmm) REVERT: D 174 MET cc_start: 0.8143 (mpp) cc_final: 0.7840 (mmm) REVERT: H 899 MET cc_start: 0.8448 (ppp) cc_final: 0.8218 (tmm) REVERT: L 233 MET cc_start: 0.7539 (ppp) cc_final: 0.7321 (ppp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1910 time to fit residues: 104.5666 Evaluate side-chains 227 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 220 optimal weight: 30.0000 chunk 318 optimal weight: 0.9980 chunk 383 optimal weight: 3.9990 chunk 417 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 338 optimal weight: 0.9980 chunk 235 optimal weight: 30.0000 chunk 491 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN G 20 GLN ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 898 HIS J 34 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.122577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.102159 restraints weight = 338024.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.101423 restraints weight = 339355.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.099395 restraints weight = 176097.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.099717 restraints weight = 174729.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099184 restraints weight = 145259.901| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 46492 Z= 0.135 Angle : 0.579 11.690 63970 Z= 0.299 Chirality : 0.042 0.332 7458 Planarity : 0.004 0.093 7530 Dihedral : 14.784 172.282 8408 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.11), residues: 5276 helix: 0.45 (0.11), residues: 2098 sheet: -0.53 (0.19), residues: 746 loop : -0.92 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.024 0.001 TYR H 346 PHE 0.084 0.002 PHE B 15 TRP 0.013 0.001 TRP D 182 HIS 0.010 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (46426) covalent geometry : angle 0.56955 / 0.30 (63914) hydrogen bonds : bond 0.04000 / 2.67 ( 2029) hydrogen bonds : angle 4.71079 / 3.28 ( 5487) metal coordination : bond 0.01515 / 1.06 ( 64) metal coordination : angle 3.54539 / 2.62 ( 56) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.977 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: B 87 MET cc_start: 0.8147 (ttt) cc_final: 0.7914 (ttt) REVERT: F 68 MET cc_start: 0.6414 (tpt) cc_final: 0.6122 (tpp) REVERT: H 601 MET cc_start: 0.7991 (mtt) cc_final: 0.7775 (mtp) REVERT: K 55 MET cc_start: 0.8578 (pmm) cc_final: 0.8306 (pmm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1651 time to fit residues: 87.7041 Evaluate side-chains 224 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 4 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 403 optimal weight: 0.0020 chunk 127 optimal weight: 0.8980 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN H 439 HIS K 157 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.122462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.102223 restraints weight = 343510.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100248 restraints weight = 328994.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.097786 restraints weight = 197872.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.098251 restraints weight = 190724.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.097878 restraints weight = 147092.573| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 46492 Z= 0.132 Angle : 0.582 15.268 63970 Z= 0.299 Chirality : 0.042 0.329 7458 Planarity : 0.004 0.085 7530 Dihedral : 14.746 173.731 8408 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.50 (0.11), residues: 5276 helix: 0.48 (0.11), residues: 2098 sheet: -0.52 (0.19), residues: 750 loop : -0.92 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 74 TYR 0.020 0.001 TYR A 32 PHE 0.064 0.002 PHE B 15 TRP 0.013 0.001 TRP D 182 HIS 0.012 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (46426) covalent geometry : angle 0.57380 / 0.30 (63914) hydrogen bonds : bond 0.03965 / 2.65 ( 2029) hydrogen bonds : angle 4.65888 / 3.24 ( 5487) metal coordination : bond 0.01528 / 1.08 ( 64) metal coordination : angle 3.26939 / 2.41 ( 56) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.997 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 67 MET cc_start: 0.7854 (tpp) cc_final: 0.7617 (tpp) REVERT: B 87 MET cc_start: 0.8250 (ttt) cc_final: 0.8021 (ttt) REVERT: G 12 MET cc_start: 0.7286 (ttp) cc_final: 0.7085 (ttm) REVERT: H 601 MET cc_start: 0.8024 (mtt) cc_final: 0.7793 (mtp) REVERT: H 633 MET cc_start: 0.8785 (ttp) cc_final: 0.8515 (ttp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1620 time to fit residues: 87.2533 Evaluate side-chains 224 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 417 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 504 optimal weight: 9.9990 chunk 519 optimal weight: 6.9990 chunk 347 optimal weight: 4.9990 chunk 337 optimal weight: 0.0170 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 302 optimal weight: 1.9990 chunk 495 optimal weight: 7.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.123002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.103979 restraints weight = 411937.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.101787 restraints weight = 339757.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.099192 restraints weight = 226807.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099745 restraints weight = 206794.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.099329 restraints weight = 150745.066| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 46492 Z= 0.111 Angle : 0.567 13.982 63970 Z= 0.291 Chirality : 0.041 0.327 7458 Planarity : 0.004 0.088 7530 Dihedral : 14.672 175.614 8408 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.43 (0.11), residues: 5276 helix: 0.53 (0.11), residues: 2102 sheet: -0.43 (0.20), residues: 720 loop : -0.89 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 74 TYR 0.018 0.001 TYR A 32 PHE 0.058 0.001 PHE B 15 TRP 0.013 0.001 TRP H 509 HIS 0.014 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (46426) covalent geometry : angle 0.56047 / 0.29 (63914) hydrogen bonds : bond 0.03766 / 2.51 ( 2029) hydrogen bonds : angle 4.56156 / 3.18 ( 5487) metal coordination : bond 0.01130 / 0.82 ( 64) metal coordination : angle 3.02062 / 2.25 ( 56) Misc. bond : bond 0.00057 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10552 Ramachandran restraints generated. 5276 Oldfield, 0 Emsley, 5276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.565 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: A 665 GLU cc_start: 0.8281 (pm20) cc_final: 0.8072 (pm20) REVERT: B 67 MET cc_start: 0.7696 (tpp) cc_final: 0.7421 (tpp) REVERT: D 55 MET cc_start: 0.8830 (pmm) cc_final: 0.8538 (pmm) REVERT: D 174 MET cc_start: 0.7648 (mmt) cc_final: 0.7319 (mmp) REVERT: E 233 MET cc_start: 0.6953 (ppp) cc_final: 0.6650 (ppp) REVERT: F 68 MET cc_start: 0.6657 (tpt) cc_final: 0.6437 (tpp) REVERT: K 67 MET cc_start: 0.8030 (ttp) cc_final: 0.7712 (ptm) REVERT: L 233 MET cc_start: 0.7087 (ppp) cc_final: 0.6739 (ppp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1626 time to fit residues: 90.6016 Evaluate side-chains 224 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 329 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 247 optimal weight: 0.0270 chunk 63 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 522 optimal weight: 20.0000 chunk 299 optimal weight: 0.0040 chunk 153 optimal weight: 8.9990 chunk 383 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 overall best weight: 0.8212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN H 81 GLN ** H 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.103622 restraints weight = 364609.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.101932 restraints weight = 337666.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099205 restraints weight = 206525.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.099831 restraints weight = 200343.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099462 restraints weight = 140450.988| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 46492 Z= 0.108 Angle : 0.564 13.420 63970 Z= 0.289 Chirality : 0.041 0.323 7458 Planarity : 0.004 0.078 7530 Dihedral : 14.591 177.240 8408 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.37 (0.11), residues: 5276 helix: 0.60 (0.11), residues: 2090 sheet: -0.39 (0.20), residues: 724 loop : -0.87 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 21 TYR 0.047 0.001 TYR H 887 PHE 0.064 0.001 PHE B 15 TRP 0.014 0.001 TRP H 509 HIS 0.012 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (46426) covalent geometry : angle 0.55774 / 0.29 (63914) hydrogen bonds : bond 0.03706 / 2.47 ( 2029) hydrogen bonds : angle 4.51417 / 3.15 ( 5487) metal coordination : bond 0.01007 / 0.72 ( 64) metal coordination : angle 2.78892 / 2.09 ( 56) Misc. bond : bond 0.00052 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6992.68 seconds wall clock time: 121 minutes 52.21 seconds (7312.21 seconds total)