Starting phenix.real_space_refine on Tue Jul 7 08:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9imk_60692/07_2026/9imk_60692.cif Found real_map, /net/cci-nas-00/data/ceres_data/9imk_60692/07_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_60692/07_2026/9imk_60692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9imk_60692/07_2026/9imk_60692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9imk_60692/07_2026/9imk_60692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9imk_60692/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 15.51, per 1000 atoms: 0.34 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: 4.00 Conformation dependent library (CDL) restraints added in 2.7 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: 5.91 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: 13.66 Time building geometry restraints manager: 5.37 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 1.475 1.377 0.098 1.50e-02 4.44e+03 4.28e+01 bond pdb=" C1' G R 41 " pdb=" N9 G R 41 " ideal model delta sigma weight residual 1.475 1.377 0.098 1.50e-02 4.44e+03 4.25e+01 bond pdb=" C1' G R 39 " pdb=" N9 G R 39 " ideal model delta sigma weight residual 1.475 1.382 0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" C1' G Q 39 " pdb=" N9 G Q 39 " ideal model delta sigma weight residual 1.475 1.383 0.092 1.50e-02 4.44e+03 3.79e+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: 7394 0.136 - 0.273: 63 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: 0.010 Normalize map: mean=0, sd=1: 10.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.330 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 63.220 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.140 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.450 ------------------------------------------------------------------------------- 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= 0.219 Angle : 0.744 31.346 63970 Z= 0.452 Chirality : 0.044 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 0.00398 / 0.22 (46426) covalent geometry : angle 0.73982 / 0.45 (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 : 1.708 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: A 211 ASP cc_start: 0.8151 (p0) cc_final: 0.7778 (p0) REVERT: A 855 MET cc_start: 0.5472 (ptt) cc_final: 0.5156 (ptm) REVERT: A 899 MET cc_start: 0.8112 (ppp) cc_final: 0.7772 (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: 0.6848 (p90) REVERT: H 855 MET cc_start: 0.6054 (ptt) cc_final: 0.4250 (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: 0.2746 time to fit residues: 183.3499 Evaluate side-chains 269 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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: 10.0000 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.120929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.101523 restraints weight = 321583.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.098481 restraints weight = 347260.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.096532 restraints weight = 254462.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.096942 restraints weight = 240893.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.096591 restraints weight = 168558.950| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 46492 Z= 0.371 Angle : 0.852 14.160 63970 Z= 0.450 Chirality : 0.050 0.281 7458 Planarity : 0.006 0.080 7530 Dihedral : 15.394 174.691 8408 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % 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: -1.22 (0.11), residues: 5276 helix: -0.24 (0.11), residues: 2072 sheet: -0.90 (0.18), residues: 762 loop : -1.19 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 A 617 HIS 0.012 0.002 HIS H 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.37 (46426) covalent geometry : angle 0.84061 / 0.45 (63914) hydrogen bonds : bond 0.06734 / 4.42 ( 2029) hydrogen bonds : angle 5.70997 / 3.96 ( 5487) metal coordination : bond 0.03975 / 2.65 ( 64) metal coordination : angle 4.73425 / 3.19 ( 56) Misc. bond : bond 0.00240 / 0.12 ( 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 342 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 1.386 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: 0.6903 (t80) cc_final: 0.6661 (t80) REVERT: A 665 GLU cc_start: 0.8364 (pm20) cc_final: 0.7493 (pm20) REVERT: A 899 MET cc_start: 0.8395 (ppp) cc_final: 0.8068 (ppp) REVERT: C 5 ASP cc_start: 0.7671 (m-30) cc_final: 0.7228 (m-30) REVERT: D 48 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: H 601 MET cc_start: 0.8459 (mtt) cc_final: 0.8161 (mtp) REVERT: H 899 MET cc_start: 0.8289 (ppp) cc_final: 0.7906 (ppp) REVERT: N 75 PHE cc_start: 0.7513 (p90) cc_final: 0.7182 (p90) outliers start: 4 outliers final: 0 residues processed: 342 average time/residue: 0.2219 time to fit residues: 126.1292 Evaluate side-chains 238 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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: 6.9990 chunk 378 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 420 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 470 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 898 HIS J 34 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 ASN M 51 ASN M 124 ASN M 164 HIS M 194 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.122374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.102431 restraints weight = 280174.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.099979 restraints weight = 312581.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.097847 restraints weight = 217202.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098276 restraints weight = 204180.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.097879 restraints weight = 149396.874| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 46492 Z= 0.211 Angle : 0.661 12.179 63970 Z= 0.349 Chirality : 0.044 0.249 7458 Planarity : 0.005 0.075 7530 Dihedral : 15.377 171.402 8408 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % 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: -0.93 (0.11), residues: 5276 helix: 0.02 (0.11), residues: 2072 sheet: -0.72 (0.19), residues: 744 loop : -1.06 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 39 TYR 0.027 0.002 TYR N 87 PHE 0.058 0.002 PHE I 15 TRP 0.013 0.002 TRP D 182 HIS 0.009 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (46426) covalent geometry : angle 0.64968 / 0.35 (63914) hydrogen bonds : bond 0.05252 / 3.49 ( 2029) hydrogen bonds : angle 5.30392 / 3.68 ( 5487) metal coordination : bond 0.02604 / 1.77 ( 64) metal coordination : angle 4.15543 / 2.99 ( 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 340 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 1.315 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: 0.6754 (t80) cc_final: 0.6520 (t80) REVERT: A 899 MET cc_start: 0.8489 (ppp) cc_final: 0.8180 (ppp) REVERT: B 62 MET cc_start: 0.7941 (ppp) cc_final: 0.7652 (ptm) REVERT: C 5 ASP cc_start: 0.7392 (m-30) cc_final: 0.6856 (m-30) REVERT: E 124 ASN cc_start: 0.0051 (OUTLIER) cc_final: -0.0159 (m-40) REVERT: G 12 MET cc_start: 0.7384 (ttt) cc_final: 0.7094 (ttm) REVERT: H 601 MET cc_start: 0.8291 (mtt) cc_final: 0.7992 (mtp) REVERT: H 855 MET cc_start: 0.5620 (ptt) cc_final: 0.4973 (ptt) REVERT: H 899 MET cc_start: 0.8344 (ppp) cc_final: 0.8079 (ppp) REVERT: K 67 MET cc_start: 0.7749 (ttt) cc_final: 0.7525 (ttt) outliers start: 4 outliers final: 1 residues processed: 340 average time/residue: 0.2120 time to fit residues: 121.7413 Evaluate side-chains 238 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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: 3.9990 chunk 354 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 422 optimal weight: 0.4980 chunk 283 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 248 optimal weight: 40.0000 chunk 403 optimal weight: 7.9990 chunk 208 optimal weight: 30.0000 chunk 365 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** H 541 GLN J 34 GLN L 124 ASN M 46 ASN M 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.122690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.103037 restraints weight = 348319.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.101136 restraints weight = 330885.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.098486 restraints weight = 212827.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098916 restraints weight = 205300.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.098627 restraints weight = 141348.508| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 46492 Z= 0.162 Angle : 0.613 11.295 63970 Z= 0.322 Chirality : 0.043 0.244 7458 Planarity : 0.005 0.139 7530 Dihedral : 15.207 170.682 8408 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % 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: -0.79 (0.11), residues: 5276 helix: 0.21 (0.11), residues: 2078 sheet: -0.76 (0.19), residues: 738 loop : -1.02 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 111 TYR 0.024 0.002 TYR A 32 PHE 0.041 0.002 PHE B 49 TRP 0.018 0.001 TRP D 182 HIS 0.011 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (46426) covalent geometry : angle 0.60219 / 0.32 (63914) hydrogen bonds : bond 0.04586 / 3.05 ( 2029) hydrogen bonds : angle 5.02230 / 3.50 ( 5487) metal coordination : bond 0.02024 / 1.36 ( 64) metal coordination : angle 3.87665 / 2.80 ( 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 333 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 330 time to evaluate : 1.502 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: 0.7546 (tpp) cc_final: 0.7330 (tpp) REVERT: A 542 MET cc_start: 0.8696 (tpp) cc_final: 0.8491 (tpt) REVERT: A 601 MET cc_start: 0.8122 (mtt) cc_final: 0.7859 (mtp) REVERT: A 899 MET cc_start: 0.8540 (ppp) cc_final: 0.8279 (ppp) REVERT: B 62 MET cc_start: 0.8007 (ppp) cc_final: 0.7805 (ptm) REVERT: D 48 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: G 12 MET cc_start: 0.7476 (ttt) cc_final: 0.7173 (ttm) REVERT: H 855 MET cc_start: 0.5784 (ptt) cc_final: 0.5037 (ptt) REVERT: H 899 MET cc_start: 0.8380 (ppp) cc_final: 0.8126 (ppp) REVERT: H 924 MET cc_start: 0.7853 (mmm) cc_final: 0.7619 (mmm) REVERT: K 67 MET cc_start: 0.7773 (ttt) cc_final: 0.7232 (ptm) outliers start: 3 outliers final: 0 residues processed: 333 average time/residue: 0.2459 time to fit residues: 137.7876 Evaluate side-chains 229 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 40.0000 chunk 216 optimal weight: 0.0770 chunk 523 optimal weight: 40.0000 chunk 434 optimal weight: 0.5980 chunk 495 optimal weight: 0.3980 chunk 302 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** 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 = 0.4472 r_free = 0.4472 target = 0.124194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.105029 restraints weight = 374671.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.103911 restraints weight = 339109.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.101760 restraints weight = 207941.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.102267 restraints weight = 196647.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.101579 restraints weight = 154158.831| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 46492 Z= 0.113 Angle : 0.574 10.038 63970 Z= 0.299 Chirality : 0.041 0.237 7458 Planarity : 0.004 0.108 7530 Dihedral : 15.012 169.580 8408 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 0.02 % Allowed : 1.19 % Favored : 98.79 % 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: -0.61 (0.11), residues: 5276 helix: 0.36 (0.11), residues: 2092 sheet: -0.61 (0.19), residues: 728 loop : -0.94 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 51 TYR 0.021 0.001 TYR A 32 PHE 0.035 0.002 PHE I 15 TRP 0.015 0.001 TRP D 182 HIS 0.013 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (46426) covalent geometry : angle 0.56599 / 0.30 (63914) hydrogen bonds : bond 0.04001 / 2.67 ( 2029) hydrogen bonds : angle 4.79076 / 3.34 ( 5487) metal coordination : bond 0.01435 / 1.00 ( 64) metal coordination : angle 3.22351 / 2.34 ( 56) Misc. bond : bond 0.00071 / 0.03 ( 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 343 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.322 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: A 899 MET cc_start: 0.8574 (ppp) cc_final: 0.8373 (ppp) REVERT: E 436 MET cc_start: -0.0820 (mmp) cc_final: -0.1980 (tpt) REVERT: G 12 MET cc_start: 0.7388 (ttt) cc_final: 0.7107 (ttm) REVERT: H 601 MET cc_start: 0.8181 (mtt) cc_final: 0.7946 (mtp) REVERT: H 855 MET cc_start: 0.5553 (ptt) cc_final: 0.5049 (ptt) REVERT: H 899 MET cc_start: 0.8430 (ppp) cc_final: 0.8185 (ppp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2140 time to fit residues: 124.3202 Evaluate side-chains 234 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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: 7.9990 chunk 160 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 789 GLN ** 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 = 0.4431 r_free = 0.4431 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.102540 restraints weight = 373763.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100626 restraints weight = 338511.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099315 restraints weight = 207605.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099443 restraints weight = 216062.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.099188 restraints weight = 149337.347| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 46492 Z= 0.208 Angle : 0.638 12.616 63970 Z= 0.334 Chirality : 0.043 0.244 7458 Planarity : 0.005 0.140 7530 Dihedral : 15.003 168.895 8408 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.72 (0.11), residues: 5276 helix: 0.27 (0.11), residues: 2098 sheet: -0.62 (0.19), residues: 736 loop : -1.03 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 248 TYR 0.022 0.002 TYR H 346 PHE 0.067 0.002 PHE D 15 TRP 0.017 0.002 TRP D 182 HIS 0.010 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (46426) covalent geometry : angle 0.63015 / 0.33 (63914) hydrogen bonds : bond 0.04672 / 3.12 ( 2029) hydrogen bonds : angle 4.93324 / 3.43 ( 5487) metal coordination : bond 0.02277 / 1.55 ( 64) metal coordination : angle 3.52945 / 2.50 ( 56) Misc. bond : bond 0.00086 / 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 308 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.737 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: 0.8303 (pm20) cc_final: 0.7619 (pm20) REVERT: E 436 MET cc_start: -0.0844 (mmp) cc_final: -0.1445 (tpt) REVERT: H 601 MET cc_start: 0.8197 (mtt) cc_final: 0.7936 (mtp) REVERT: H 899 MET cc_start: 0.8541 (ppp) cc_final: 0.8332 (ppp) REVERT: I 72 LYS cc_start: 0.9444 (pptt) cc_final: 0.9237 (pptt) REVERT: K 67 MET cc_start: 0.7643 (ptm) cc_final: 0.7337 (ptm) REVERT: L 233 MET cc_start: 0.7147 (ppp) cc_final: 0.6946 (ppp) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2241 time to fit residues: 117.6747 Evaluate side-chains 221 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 0.0970 chunk 463 optimal weight: 0.0060 chunk 111 optimal weight: 0.7980 chunk 414 optimal weight: 3.9990 chunk 304 optimal weight: 0.6980 chunk 482 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 492 optimal weight: 40.0000 chunk 60 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 213 optimal weight: 50.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 164 HIS F 245 HIS F 275 GLN H 898 HIS I 118 ASN K 100 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.101669 restraints weight = 295196.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.098433 restraints weight = 294509.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095001 restraints weight = 180988.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.094498 restraints weight = 178637.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.094733 restraints weight = 149965.445| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 46492 Z= 0.112 Angle : 0.579 10.487 63970 Z= 0.299 Chirality : 0.041 0.236 7458 Planarity : 0.004 0.115 7530 Dihedral : 14.899 168.514 8408 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.57 (0.11), residues: 5276 helix: 0.43 (0.11), residues: 2092 sheet: -0.59 (0.19), residues: 748 loop : -0.95 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.020 0.001 TYR A 32 PHE 0.046 0.002 PHE B 15 TRP 0.015 0.001 TRP A 509 HIS 0.011 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (46426) covalent geometry : angle 0.56855 / 0.30 (63914) hydrogen bonds : bond 0.03882 / 2.59 ( 2029) hydrogen bonds : angle 4.68347 / 3.27 ( 5487) metal coordination : bond 0.01749 / 1.29 ( 64) metal coordination : angle 3.70846 / 2.82 ( 56) Misc. bond : bond 0.00066 / 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 327 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.071 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: 0.7193 (tpp) cc_final: 0.6931 (tpp) REVERT: A 899 MET cc_start: 0.8620 (ppp) cc_final: 0.8373 (ppp) REVERT: B 174 MET cc_start: 0.7666 (tmm) cc_final: 0.7460 (tmm) REVERT: D 55 MET cc_start: 0.8780 (pmm) cc_final: 0.8528 (pmm) REVERT: E 233 MET cc_start: 0.7733 (ppp) cc_final: 0.7510 (ppp) REVERT: E 436 MET cc_start: -0.2174 (mmp) cc_final: -0.2819 (tpt) REVERT: H 899 MET cc_start: 0.8657 (ppp) cc_final: 0.8437 (ppp) REVERT: I 62 MET cc_start: 0.8286 (ppp) cc_final: 0.7952 (ppp) REVERT: L 233 MET cc_start: 0.7977 (ppp) cc_final: 0.7720 (ppp) REVERT: N 75 PHE cc_start: 0.7487 (p90) cc_final: 0.7099 (p90) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1639 time to fit residues: 92.3835 Evaluate side-chains 228 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 10.0000 chunk 318 optimal weight: 0.8980 chunk 383 optimal weight: 6.9990 chunk 417 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 413 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 491 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 275 GLN ** H 789 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.101702 restraints weight = 337481.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.099086 restraints weight = 323743.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096767 restraints weight = 213053.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.097250 restraints weight = 200458.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.096943 restraints weight = 137355.588| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 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 = 0.3916 r_free = 0.3916 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: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46492 Z= 0.160 Angle : 0.595 11.505 63970 Z= 0.309 Chirality : 0.042 0.239 7458 Planarity : 0.004 0.096 7530 Dihedral : 14.844 169.706 8408 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.55 (0.11), residues: 5276 helix: 0.43 (0.11), residues: 2098 sheet: -0.56 (0.19), residues: 754 loop : -0.93 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 74 TYR 0.030 0.001 TYR H 903 PHE 0.066 0.002 PHE B 49 TRP 0.015 0.001 TRP D 182 HIS 0.009 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (46426) covalent geometry : angle 0.58561 / 0.31 (63914) hydrogen bonds : bond 0.04173 / 2.78 ( 2029) hydrogen bonds : angle 4.74894 / 3.31 ( 5487) metal coordination : bond 0.01926 / 1.35 ( 64) metal coordination : angle 3.64917 / 2.68 ( 56) Misc. bond : bond 0.00070 / 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 311 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 MET cc_start: 0.8519 (ppp) cc_final: 0.8306 (ppp) REVERT: E 436 MET cc_start: -0.1241 (mmp) cc_final: -0.1795 (tpt) REVERT: H 124 MET cc_start: 0.8275 (mtp) cc_final: 0.8073 (mtt) REVERT: H 601 MET cc_start: 0.8042 (mtt) cc_final: 0.7837 (mtp) REVERT: L 233 MET cc_start: 0.7461 (ppp) cc_final: 0.7222 (ppp) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1713 time to fit residues: 90.7809 Evaluate side-chains 218 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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: 7.9990 chunk 232 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 201 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 326 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 403 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 275 GLN K 157 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN N 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.102241 restraints weight = 343591.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.099662 restraints weight = 324943.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096732 restraints weight = 216768.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097328 restraints weight = 191779.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.097077 restraints weight = 137996.104| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 46492 Z= 0.132 Angle : 0.577 11.448 63970 Z= 0.299 Chirality : 0.041 0.237 7458 Planarity : 0.004 0.088 7530 Dihedral : 14.803 171.942 8408 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % 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: -0.49 (0.11), residues: 5276 helix: 0.49 (0.11), residues: 2098 sheet: -0.52 (0.19), residues: 750 loop : -0.91 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 533 TYR 0.024 0.001 TYR H 903 PHE 0.055 0.002 PHE B 49 TRP 0.014 0.001 TRP A 598 HIS 0.009 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (46426) covalent geometry : angle 0.56891 / 0.30 (63914) hydrogen bonds : bond 0.03902 / 2.60 ( 2029) hydrogen bonds : angle 4.64039 / 3.24 ( 5487) metal coordination : bond 0.01542 / 1.09 ( 64) metal coordination : angle 3.34656 / 2.46 ( 56) Misc. bond : bond 0.00059 / 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 305 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.029 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: E 274 MET cc_start: 0.2424 (ttm) cc_final: 0.2056 (mmm) REVERT: E 436 MET cc_start: -0.1340 (mmp) cc_final: -0.1842 (tpt) REVERT: H 601 MET cc_start: 0.8099 (mtt) cc_final: 0.7850 (mtp) REVERT: L 233 MET cc_start: 0.7440 (ppp) cc_final: 0.7231 (ppp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1661 time to fit residues: 86.8024 Evaluate side-chains 223 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 2.9990 chunk 322 optimal weight: 0.7980 chunk 504 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 495 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** ** 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 275 GLN H 439 HIS ** 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 = 0.4446 r_free = 0.4446 target = 0.122183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.102824 restraints weight = 408846.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.101113 restraints weight = 333152.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.098463 restraints weight = 222471.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.099062 restraints weight = 215860.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.098536 restraints weight = 151944.358| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 46492 Z= 0.139 Angle : 0.579 10.238 63970 Z= 0.301 Chirality : 0.041 0.237 7458 Planarity : 0.004 0.086 7530 Dihedral : 14.763 172.818 8408 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.49 (0.11), residues: 2096 sheet: -0.52 (0.19), residues: 750 loop : -0.93 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.047 0.001 TYR H 887 PHE 0.053 0.002 PHE B 49 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 0.00309 / 0.14 (46426) covalent geometry : angle 0.57098 / 0.30 (63914) hydrogen bonds : bond 0.03972 / 2.64 ( 2029) hydrogen bonds : angle 4.65198 / 3.25 ( 5487) metal coordination : bond 0.01569 / 1.10 ( 64) metal coordination : angle 3.23080 / 2.37 ( 56) Misc. bond : bond 0.00065 / 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 299 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.995 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: A 629 MET cc_start: 0.8194 (mmm) cc_final: 0.7986 (mmt) REVERT: D 55 MET cc_start: 0.8815 (pmm) cc_final: 0.8490 (pmm) REVERT: E 233 MET cc_start: 0.7000 (ppp) cc_final: 0.6683 (ppp) REVERT: E 274 MET cc_start: 0.2462 (ttm) cc_final: 0.2144 (mmm) REVERT: E 436 MET cc_start: -0.1200 (mmp) cc_final: -0.1739 (tpt) REVERT: H 542 MET cc_start: 0.8381 (tpp) cc_final: 0.8146 (mmt) REVERT: L 233 MET cc_start: 0.7383 (ppp) cc_final: 0.7178 (ppp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1586 time to fit residues: 81.6007 Evaluate side-chains 221 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 0.9980 chunk 230 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 247 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 522 optimal weight: 20.0000 chunk 299 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 chunk 383 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.122737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.103336 restraints weight = 356331.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.101723 restraints weight = 339397.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.099308 restraints weight = 213353.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.099878 restraints weight = 205047.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.099263 restraints weight = 156032.128| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.32 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: 0.6950 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46492 Z= 0.113 Angle : 0.567 9.456 63970 Z= 0.292 Chirality : 0.041 0.235 7458 Planarity : 0.004 0.080 7530 Dihedral : 14.699 174.558 8408 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.38 (0.12), residues: 5276 helix: 0.59 (0.11), residues: 2090 sheet: -0.41 (0.20), residues: 728 loop : -0.88 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.038 0.001 TYR H 887 PHE 0.076 0.001 PHE B 49 TRP 0.013 0.001 TRP A 509 HIS 0.013 0.001 HIS H 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (46426) covalent geometry : angle 0.56010 / 0.29 (63914) hydrogen bonds : bond 0.03753 / 2.50 ( 2029) hydrogen bonds : angle 4.55351 / 3.18 ( 5487) metal coordination : bond 0.01248 / 0.91 ( 64) metal coordination : angle 2.98409 / 2.21 ( 56) Misc. bond : bond 0.00058 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6769.56 seconds wall clock time: 118 minutes 20.50 seconds (7100.50 seconds total)