Starting phenix.real_space_refine on Sat Jan 20 05:10:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zeb_14688/01_2024/7zeb_14688_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.030 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 15 5.49 5 S 466 5.16 5 C 42818 2.51 5 N 11178 2.21 5 O 11889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 GLU 182": "OE1" <-> "OE2" Residue "4 GLU 227": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "k GLU 213": "OE1" <-> "OE2" Residue "k GLU 229": "OE1" <-> "OE2" Residue "l GLU 36": "OE1" <-> "OE2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l GLU 88": "OE1" <-> "OE2" Residue "n GLU 24": "OE1" <-> "OE2" Residue "o GLU 99": "OE1" <-> "OE2" Residue "s GLU 118": "OE1" <-> "OE2" Residue "t GLU 69": "OE1" <-> "OE2" Residue "t GLU 122": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "x GLU 41": "OE1" <-> "OE2" Residue "y GLU 47": "OE1" <-> "OE2" Residue "1 GLU 226": "OE1" <-> "OE2" Residue "1 GLU 427": "OE1" <-> "OE2" Residue "3 GLU 261": "OE1" <-> "OE2" Residue "3 GLU 372": "OE1" <-> "OE2" Residue "3 GLU 445": "OE1" <-> "OE2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "9 GLU 164": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 107": "OE1" <-> "OE2" Residue "d GLU 162": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "f GLU 21": "OE1" <-> "OE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 108": "OE1" <-> "OE2" Residue "i GLU 2": "OE1" <-> "OE2" Residue "j GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66396 Number of models: 1 Model: "" Number of chains: 60 Chain: "4" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3404 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 396} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1198 Classifications: {'peptide': 150} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 139} Chain: "9" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1376 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2662 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 20, 'TRANS': 310} Chain breaks: 1 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 619 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44055 SG CYS 1 365 97.548 54.963 240.192 1.00 32.33 S ATOM 44379 SG CYS 1 405 100.502 49.198 239.176 1.00 25.21 S ATOM 44035 SG CYS 1 362 100.162 54.338 234.999 1.00 63.58 S ATOM 44016 SG CYS 1 359 104.303 54.228 240.239 1.00 34.60 S ATOM 45456 SG CYS 2 103 95.777 49.469 259.813 1.00 78.23 S ATOM 45490 SG CYS 2 108 93.633 47.315 261.663 1.00 39.46 S ATOM 45770 SG CYS 2 144 97.077 45.955 256.068 1.00 89.13 S ATOM 45793 SG CYS 2 148 95.011 43.345 257.301 1.00 55.45 S ATOM 47133 SG CYS 3 114 100.828 73.607 225.824 1.00 12.74 S ATOM 47072 SG CYS 3 105 96.112 77.517 228.268 1.00 22.15 S ATOM 47093 SG CYS 3 108 102.284 78.526 229.772 1.00 42.48 S ATOM 47465 SG CYS 3 156 108.033 65.246 230.179 1.00 27.40 S ATOM 47442 SG CYS 3 153 106.370 68.342 235.657 1.00 9.11 S ATOM 47489 SG CYS 3 159 112.575 68.776 233.454 1.00 40.62 S ATOM 47819 SG CYS 3 203 108.053 71.711 230.252 1.00 89.53 S ATOM 46578 SG CYS 3 41 105.791 58.960 227.912 1.00 90.06 S ATOM 46664 SG CYS 3 52 102.491 60.078 227.278 1.00 65.64 S ATOM 46689 SG CYS 3 55 102.447 55.142 223.650 1.00 31.27 S ATOM 46790 SG CYS 3 69 105.928 54.961 225.036 1.00 98.67 S ATOM 54012 SG CYS 6 119 86.332 101.448 204.048 1.00 34.81 S ATOM 54242 SG CYS 6 149 83.507 99.597 209.388 1.00 50.87 S ATOM 53514 SG CYS 6 55 81.259 105.035 206.317 1.00 11.84 S ATOM 53508 SG CYS 6 54 79.802 99.446 204.053 1.00 30.23 S ATOM 55396 SG CYS 9 116 88.221 99.373 215.761 1.00 62.18 S ATOM 55443 SG CYS 9 122 88.875 94.844 220.482 1.00 15.82 S ATOM 55170 SG CYS 9 87 92.329 94.420 214.941 1.00 56.81 S ATOM 55472 SG CYS 9 126 90.969 91.379 227.746 1.00 26.72 S ATOM 55143 SG CYS 9 83 94.599 92.795 222.465 1.00 10.82 S ATOM 55101 SG CYS 9 77 97.084 93.822 228.293 1.00 30.15 S ATOM 55120 SG CYS 9 80 95.649 87.579 226.069 1.00 24.32 S ATOM 56719 SG CYS b 59 93.094 86.115 243.191 1.00 82.41 S ATOM 56897 SG CYS b 84 95.981 86.248 240.591 1.00 65.57 S ATOM 56919 SG CYS b 87 94.743 88.741 241.772 1.00 51.01 S Time building chain proxies: 25.90, per 1000 atoms: 0.39 Number of scatterers: 66396 At special positions: 0 Unit cell: (170.8, 201.3, 290.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 466 16.00 P 15 15.00 O 11889 8.00 N 11178 7.00 C 42818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.76 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 300 " pdb="FE2 SF4 6 300 " - pdb=" SG CYS 6 149 " pdb="FE1 SF4 6 300 " - pdb=" SG CYS 6 119 " pdb="FE4 SF4 6 300 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 300 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 202 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 80 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 332 helices and 30 sheets defined 49.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.53 Creating SS restraints... Processing helix chain '4' and resid 8 through 13 Processing helix chain '4' and resid 87 through 90 No H-bonds generated for 'chain '4' and resid 87 through 90' Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix removed outlier: 4.047A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 185 removed outlier: 4.363A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.354A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 262 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 278 through 280 No H-bonds generated for 'chain '4' and resid 278 through 280' Processing helix chain '4' and resid 293 through 315 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.306A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 Processing helix chain '4' and resid 425 through 429 Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.581A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 Proline residue: A 74 - end of helix removed outlier: 6.151A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 30 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 56 removed outlier: 3.522A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.229A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 4.430A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 170 removed outlier: 3.929A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 165 through 170' Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 219 through 242 removed outlier: 4.032A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 73 Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.686A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 removed outlier: 3.757A pdb=" N THR J 172 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG J 173 " --> pdb=" O MET J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 76 removed outlier: 4.218A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 5.174A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 82 No H-bonds generated for 'chain 'K' and resid 79 through 82' Processing helix chain 'L' and resid 3 through 23 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 237 removed outlier: 4.250A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.271A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 272 through 293 Processing helix chain 'L' and resid 298 through 317 Processing helix chain 'L' and resid 322 through 350 removed outlier: 3.772A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 3.575A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 removed outlier: 5.855A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.910A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 532 Proline residue: L 530 - end of helix Processing helix chain 'L' and resid 536 through 546 Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.050A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 125 through 135 removed outlier: 3.855A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 170 removed outlier: 3.546A pdb=" N LEU M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR M 152 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.954A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.437A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 218 removed outlier: 3.924A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 214 through 218' Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.680A pdb=" N LEU M 238 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 239 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG M 245 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.544A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.972A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.176A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 120 Processing helix chain 'N' and resid 124 through 135 removed outlier: 5.154A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 171 removed outlier: 4.271A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 191 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.559A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 250 Processing helix chain 'N' and resid 258 through 269 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.665A pdb=" N LYS N 312 " --> pdb=" O ASN N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 340 through 346 Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 18 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 87 through 103 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.303A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 57 through 76 removed outlier: 3.738A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 removed outlier: 3.787A pdb=" N LYS Z 57 " --> pdb=" O ARG Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 115 removed outlier: 4.942A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 117 through 123 removed outlier: 4.034A pdb=" N HIS Z 120 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG Z 121 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN Z 122 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN Z 123 " --> pdb=" O HIS Z 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 117 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 14 through 16 No H-bonds generated for 'chain 'k' and resid 14 through 16' Processing helix chain 'k' and resid 38 through 45 removed outlier: 3.593A pdb=" N LYS k 45 " --> pdb=" O GLU k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 160 Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 189 through 191 No H-bonds generated for 'chain 'k' and resid 189 through 191' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 211 through 217 removed outlier: 5.617A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 225 through 228 No H-bonds generated for 'chain 'k' and resid 225 through 228' Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 272 removed outlier: 4.928A pdb=" N TYR k 272 " --> pdb=" O GLU k 268 " (cutoff:3.500A) Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 48 through 54 Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 98 No H-bonds generated for 'chain 'l' and resid 95 through 98' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 46 Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 37 Processing helix chain 'n' and resid 49 through 52 Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.814A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 93 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 124 Processing helix chain 'q' and resid 129 through 135 Processing helix chain 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 3 through 7 Processing helix chain 's' and resid 42 through 46 Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 60 through 71 Processing helix chain 's' and resid 80 through 120 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 96 Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 4.624A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 64 Processing helix chain 'w' and resid 70 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 5.948A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 30 removed outlier: 3.714A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix Processing helix chain 'y' and resid 32 through 34 No H-bonds generated for 'chain 'y' and resid 32 through 34' Processing helix chain 'z' and resid 2 through 16 Proline residue: z 7 - end of helix Processing helix chain 'z' and resid 18 through 27 Processing helix chain 'z' and resid 42 through 55 Processing helix chain '1' and resid 33 through 39 removed outlier: 3.684A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.362A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 removed outlier: 4.318A pdb=" N SER 1 231 " --> pdb=" O THR 1 227 " (cutoff:3.500A) Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 309 through 314 removed outlier: 3.531A pdb=" N GLU 1 313 " --> pdb=" O LYS 1 309 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR 1 314 " --> pdb=" O SER 1 310 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 309 through 314' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.551A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.112A pdb=" N ASP 1 390 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER 1 391 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.216A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 159 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 197 through 202 Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 271 through 274 No H-bonds generated for 'chain '3' and resid 271 through 274' Processing helix chain '3' and resid 296 through 308 Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 373 Processing helix chain '3' and resid 389 through 400 Processing helix chain '3' and resid 426 through 433 removed outlier: 4.018A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 456 through 458 No H-bonds generated for 'chain '3' and resid 456 through 458' Processing helix chain '3' and resid 463 through 480 removed outlier: 3.537A pdb=" N THR 3 479 " --> pdb=" O GLN 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 497 through 505 removed outlier: 4.610A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 650 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '5' and resid 17 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 5.064A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 4.667A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 126 through 137 removed outlier: 5.674A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 119 through 122 No H-bonds generated for 'chain '6' and resid 119 through 122' Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 15 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 83 through 86 No H-bonds generated for 'chain '9' and resid 83 through 86' Processing helix chain '9' and resid 122 through 125 No H-bonds generated for 'chain '9' and resid 122 through 125' Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.722A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.571A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 Processing helix chain 'b' and resid 40 through 44 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 28 through 31 No H-bonds generated for 'chain 'c' and resid 28 through 31' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 30 through 39 Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.559A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 84 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 184 Processing helix chain 'd' and resid 194 through 197 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 300 through 303 removed outlier: 3.566A pdb=" N LEU d 303 " --> pdb=" O LEU d 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 300 through 303' Processing helix chain 'd' and resid 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 314 through 318 Processing helix chain 'd' and resid 324 through 326 No H-bonds generated for 'chain 'd' and resid 324 through 326' Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.990A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.159A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 64 through 70 Processing helix chain 'f' and resid 76 through 96 Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 2 through 16 Processing helix chain 'i' and resid 20 through 29 Processing helix chain 'i' and resid 84 through 90 Processing helix chain 'j' and resid 8 through 20 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 66 No H-bonds generated for 'chain 'j' and resid 64 through 66' Processing helix chain 'j' and resid 73 through 83 Processing sheet with id= A, first strand: chain '4' and resid 47 through 51 Processing sheet with id= B, first strand: chain '4' and resid 361 through 369 Processing sheet with id= C, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= D, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= E, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.665A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.674A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '1' and resid 219 through 224 removed outlier: 6.639A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 266 through 271 Processing sheet with id= I, first strand: chain '2' and resid 137 through 142 removed outlier: 6.877A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 9 through 13 Processing sheet with id= K, first strand: chain '3' and resid 56 through 58 Processing sheet with id= L, first strand: chain '3' and resid 146 through 148 Processing sheet with id= M, first strand: chain '3' and resid 173 through 175 Processing sheet with id= N, first strand: chain '3' and resid 223 through 228 Processing sheet with id= O, first strand: chain '3' and resid 283 through 285 Processing sheet with id= P, first strand: chain '3' and resid 343 through 345 removed outlier: 8.315A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '3' and resid 405 through 409 Processing sheet with id= R, first strand: chain '3' and resid 572 through 574 Processing sheet with id= S, first strand: chain '5' and resid 74 through 82 removed outlier: 6.782A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '5' and resid 172 through 177 Processing sheet with id= U, first strand: chain '6' and resid 85 through 88 removed outlier: 6.613A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '9' and resid 65 through 67 Processing sheet with id= W, first strand: chain '9' and resid 92 through 98 removed outlier: 5.776A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= Y, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Z, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= AA, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AB, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.669A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.858A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.268A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 2818 hydrogen bonds defined for protein. 7932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.27 Time building geometry restraints manager: 23.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28184 1.42 - 1.64: 39067 1.64 - 1.86: 758 1.86 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 68089 Sorted by residual: bond pdb=" O2B NDP d 402 " pdb=" P2B NDP d 402 " ideal model delta sigma weight residual 1.833 1.618 0.215 3.80e-02 6.93e+02 3.21e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.340 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C13 ZMP j 101 " pdb=" N1 ZMP j 101 " ideal model delta sigma weight residual 1.451 1.340 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.342 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.452 1.349 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 68084 not shown) Histogram of bond angle deviations from ideal: 70.05 - 83.47: 78 83.47 - 96.88: 3 96.88 - 110.29: 15239 110.29 - 123.71: 74793 123.71 - 137.12: 2205 Bond angle restraints: 92318 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 74.36 46.24 3.00e+00 1.11e-01 2.38e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 71.17 38.13 3.00e+00 1.11e-01 1.62e+02 angle pdb=" PA NDP d 402 " pdb=" O3 NDP d 402 " pdb=" PN NDP d 402 " ideal model delta sigma weight residual 107.74 131.99 -24.25 1.95e+00 2.62e-01 1.54e+02 angle pdb=" C5B NDP d 402 " pdb=" O5B NDP d 402 " pdb=" PA NDP d 402 " ideal model delta sigma weight residual 103.84 119.97 -16.13 1.91e+00 2.73e-01 7.09e+01 angle pdb=" CA PRO v 17 " pdb=" N PRO v 17 " pdb=" CD PRO v 17 " ideal model delta sigma weight residual 112.00 101.51 10.49 1.40e+00 5.10e-01 5.62e+01 ... (remaining 92313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 39323 34.15 - 68.29: 1540 68.29 - 102.44: 98 102.44 - 136.59: 1 136.59 - 170.73: 1 Dihedral angle restraints: 40963 sinusoidal: 17088 harmonic: 23875 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -141.51 -38.49 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CB CYS s 58 " pdb=" SG CYS s 58 " pdb=" SG CYS s 89 " pdb=" CB CYS s 89 " ideal model delta sinusoidal sigma weight residual -86.00 -149.81 63.81 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS l 42 " pdb=" SG CYS l 42 " pdb=" SG CYS l 55 " pdb=" CB CYS l 55 " ideal model delta sinusoidal sigma weight residual 93.00 153.35 -60.35 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 40960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.243: 10100 4.243 - 8.487: 0 8.487 - 12.730: 0 12.730 - 16.973: 0 16.973 - 21.217: 24 Chirality restraints: 10124 Sorted by residual: chirality pdb="FE4 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S3 SF4 6 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.66 21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S4 SF4 6 300 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 9 202 " pdb=" S1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S4 SF4 9 202 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10121 not shown) Planarity restraints: 11635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR v 16 " -0.107 5.00e-02 4.00e+02 1.54e-01 3.81e+01 pdb=" N PRO v 17 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO v 17 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO v 17 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY q 16 " -0.090 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO q 17 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO q 17 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO q 17 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN 3 259 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ASN 3 259 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN 3 259 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU 3 260 " 0.021 2.00e-02 2.50e+03 ... (remaining 11632 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 15866 2.79 - 3.38: 71070 3.38 - 3.96: 128472 3.96 - 4.55: 177941 4.55 - 5.14: 265923 Nonbonded interactions: 659272 Sorted by model distance: nonbonded pdb=" O LEU N 337 " pdb=" OG1 THR N 340 " model vdw 2.202 2.440 nonbonded pdb=" O ILE 4 151 " pdb=" OG1 THR 4 155 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR L 162 " pdb=" OD1 ASN v 87 " model vdw 2.227 2.440 nonbonded pdb=" OD2 ASP 3 272 " pdb=" OG1 THR 3 683 " model vdw 2.246 2.440 nonbonded pdb=" OG SER p 25 " pdb=" OE1 GLU p 27 " model vdw 2.256 2.440 ... (remaining 659267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and (resid 5 through 25 or resid 31 through 86 or resid 101)) selection = (chain 'j' and (resid 5 through 86 or (resid 101 and (name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 o \ r name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or n \ ame O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or name \ S1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 4.260 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 154.280 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.290 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.215 68089 Z= 0.291 Angle : 0.849 46.245 92318 Z= 0.414 Chirality : 1.030 21.217 10124 Planarity : 0.006 0.154 11635 Dihedral : 16.917 170.731 25545 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.81 % Favored : 96.18 % Rotamer: Outliers : 0.46 % Allowed : 23.62 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.09), residues: 8082 helix: -0.05 (0.07), residues: 4155 sheet: -0.26 (0.27), residues: 402 loop : -0.99 (0.10), residues: 3525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP v 73 HIS 0.009 0.001 HIS j 35 PHE 0.032 0.001 PHE L 335 TYR 0.040 0.001 TYR p 101 ARG 0.021 0.000 ARG t 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 798 time to evaluate : 5.765 Fit side-chains revert: symmetry clash REVERT: 4 314 CYS cc_start: 0.8730 (m) cc_final: 0.8327 (t) REVERT: 4 342 MET cc_start: 0.9345 (tpt) cc_final: 0.8953 (tpp) REVERT: A 44 MET cc_start: 0.4946 (mpp) cc_final: 0.4678 (tpt) REVERT: J 169 MET cc_start: 0.8800 (tpt) cc_final: 0.8406 (mmm) REVERT: M 243 MET cc_start: 0.8748 (mmp) cc_final: 0.8510 (mmp) REVERT: M 329 LEU cc_start: 0.9229 (mm) cc_final: 0.9005 (mm) REVERT: M 441 MET cc_start: 0.9161 (tpp) cc_final: 0.8861 (tpp) REVERT: N 14 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7081 (mpt) REVERT: N 215 MET cc_start: 0.8570 (tpt) cc_final: 0.8312 (tpp) REVERT: V 117 MET cc_start: 0.6422 (mpp) cc_final: 0.6191 (pmm) REVERT: k 2 GLN cc_start: 0.8519 (pp30) cc_final: 0.7980 (pt0) REVERT: k 182 ARG cc_start: 0.6709 (tpp80) cc_final: 0.6422 (tpp80) REVERT: k 249 LEU cc_start: 0.8480 (pp) cc_final: 0.8133 (mt) REVERT: o 10 PRO cc_start: 0.8938 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: o 90 MET cc_start: 0.8490 (ttm) cc_final: 0.8277 (ttt) REVERT: q 23 ASN cc_start: 0.7037 (t0) cc_final: 0.6584 (p0) REVERT: s 117 ARG cc_start: 0.7046 (tmm160) cc_final: 0.6703 (mtt180) REVERT: v 83 MET cc_start: 0.8664 (ttm) cc_final: 0.8430 (ttp) REVERT: y 31 ASP cc_start: 0.8704 (p0) cc_final: 0.8436 (p0) REVERT: z 43 TYR cc_start: 0.8835 (t80) cc_final: 0.8597 (t80) REVERT: 3 54 MET cc_start: 0.9400 (tpt) cc_final: 0.9134 (tpt) REVERT: f 70 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7830 (tt0) REVERT: j 49 GLU cc_start: 0.6880 (pt0) cc_final: 0.6420 (pt0) outliers start: 33 outliers final: 14 residues processed: 817 average time/residue: 0.6188 time to fit residues: 870.1729 Evaluate side-chains 763 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 748 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 405 LEU Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain d residue 243 GLN Chi-restraints excluded: chain h residue 111 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 408 optimal weight: 20.0000 chunk 323 optimal weight: 30.0000 chunk 626 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 466 optimal weight: 20.0000 chunk 725 optimal weight: 2.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 27 HIS ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 ASN M 26 ASN ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN N 289 ASN l 20 GLN p 116 GLN y 13 HIS 3 259 ASN ** 5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 2 HIS d 119 GLN h 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.272 68089 Z= 0.628 Angle : 1.577 51.346 92318 Z= 1.020 Chirality : 0.307 6.549 10124 Planarity : 0.005 0.086 11635 Dihedral : 7.056 170.847 9384 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 3.70 % Allowed : 21.89 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.09), residues: 8082 helix: 0.69 (0.08), residues: 4180 sheet: -0.27 (0.26), residues: 417 loop : -0.83 (0.11), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 26 HIS 0.007 0.001 HIS b 68 PHE 0.028 0.001 PHE N 292 TYR 0.019 0.001 TYR L 422 ARG 0.008 0.000 ARG Y 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 751 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 71 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6231 (mt-10) REVERT: J 128 TYR cc_start: 0.6616 (t80) cc_final: 0.6335 (m-80) REVERT: L 272 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5384 (t80) REVERT: M 76 MET cc_start: 0.9154 (mtp) cc_final: 0.8938 (mtp) REVERT: M 141 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7696 (pm20) REVERT: M 271 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mpp) REVERT: M 395 LEU cc_start: 0.8690 (mt) cc_final: 0.8403 (mt) REVERT: N 14 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7337 (mpt) REVERT: N 282 MET cc_start: 0.8331 (mtp) cc_final: 0.8088 (mtp) REVERT: V 117 MET cc_start: 0.6640 (mpp) cc_final: 0.6293 (mpp) REVERT: k 107 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: l 82 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6406 (ttp-170) REVERT: m 82 ARG cc_start: 0.7503 (mmt-90) cc_final: 0.6976 (mmp-170) REVERT: o 1 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7022 (ppp) REVERT: p 30 LYS cc_start: 0.8648 (mttp) cc_final: 0.8307 (mmtm) REVERT: p 109 ASP cc_start: 0.7849 (m-30) cc_final: 0.7648 (m-30) REVERT: q 33 SER cc_start: 0.8766 (m) cc_final: 0.8202 (t) REVERT: s 94 TYR cc_start: 0.8727 (t80) cc_final: 0.8456 (t80) REVERT: s 117 ARG cc_start: 0.7109 (tmm160) cc_final: 0.6723 (mpt-90) REVERT: v 83 MET cc_start: 0.8683 (ttm) cc_final: 0.8414 (ttp) REVERT: 1 107 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8774 (m-30) REVERT: 1 429 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7552 (tpp80) REVERT: 2 72 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7523 (mp) REVERT: 2 78 MET cc_start: 0.8911 (tpt) cc_final: 0.8430 (tpp) REVERT: 3 59 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8669 (mm) REVERT: 5 46 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8315 (p) REVERT: e 37 GLU cc_start: 0.9223 (tp30) cc_final: 0.8946 (tp30) REVERT: f 34 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8394 (mp) REVERT: f 66 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7615 (ttpt) REVERT: f 67 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7409 (mm) outliers start: 265 outliers final: 148 residues processed: 937 average time/residue: 0.6075 time to fit residues: 984.4244 Evaluate side-chains 884 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 722 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 71 GLU Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 144 ILE Chi-restraints excluded: chain 4 residue 145 THR Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 415 VAL Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 271 MET Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 208 TYR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain V residue 65 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 86 GLU Chi-restraints excluded: chain Z residue 123 ASN Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 107 GLN Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 144 ILE Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 62 MET Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 27 THR Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 49 MET Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 26 LEU Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 116 ASP Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain v residue 40 ASP Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 91 THR Chi-restraints excluded: chain v residue 153 VAL Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 50 ASP Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 118 ILE Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain 1 residue 50 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 189 GLU Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 1 residue 429 ARG Chi-restraints excluded: chain 2 residue 22 ASP Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 3 residue 37 ILE Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 108 CYS Chi-restraints excluded: chain 3 residue 248 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 675 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 45 PHE Chi-restraints excluded: chain 5 residue 46 SER Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 59 MET Chi-restraints excluded: chain 9 residue 36 MET Chi-restraints excluded: chain 9 residue 138 GLU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain c residue 121 ASN Chi-restraints excluded: chain d residue 171 ILE Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 243 GLN Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 327 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 34 LEU Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 92 THR Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 66 SER Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 81 MET Chi-restraints excluded: chain i residue 94 THR Chi-restraints excluded: chain i residue 111 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 603 optimal weight: 5.9990 chunk 494 optimal weight: 20.0000 chunk 200 optimal weight: 0.9980 chunk 726 optimal weight: 1.9990 chunk 785 optimal weight: 2.9990 chunk 647 optimal weight: 0.9980 chunk 720 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 583 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN L 479 GLN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN Y 105 GLN k 287 HIS n 32 GLN q 60 GLN 2 121 GLN ** 5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 68089 Z= 0.566 Angle : 1.554 50.852 92318 Z= 1.010 Chirality : 0.310 6.428 10124 Planarity : 0.004 0.067 11635 Dihedral : 6.691 170.327 9371 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 22.84 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.10), residues: 8082 helix: 1.10 (0.08), residues: 4180 sheet: -0.19 (0.26), residues: 421 loop : -0.67 (0.11), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP w 26 HIS 0.004 0.001 HIS 3 101 PHE 0.025 0.001 PHE L 335 TYR 0.022 0.001 TYR L 422 ARG 0.004 0.000 ARG q 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 770 time to evaluate : 5.879 Fit side-chains revert: symmetry clash REVERT: 4 71 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6087 (mt-10) REVERT: J 99 MET cc_start: 0.7172 (mmm) cc_final: 0.6964 (mmm) REVERT: L 272 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5276 (t80) REVERT: L 571 MET cc_start: 0.8294 (mmt) cc_final: 0.8038 (mmt) REVERT: M 76 MET cc_start: 0.9086 (mtp) cc_final: 0.8858 (mtp) REVERT: M 271 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8851 (mpp) REVERT: M 395 LEU cc_start: 0.8661 (mt) cc_final: 0.8397 (mt) REVERT: M 458 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7699 (pp) REVERT: N 251 MET cc_start: 0.8792 (mtm) cc_final: 0.8557 (mtm) REVERT: N 294 MET cc_start: 0.8799 (tpp) cc_final: 0.8578 (mmm) REVERT: V 117 MET cc_start: 0.6789 (mpp) cc_final: 0.6351 (mpp) REVERT: Y 67 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7981 (tt) REVERT: k 107 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7203 (tp40) REVERT: k 182 ARG cc_start: 0.6648 (tpp80) cc_final: 0.6371 (tpp80) REVERT: k 191 GLU cc_start: 0.8581 (pt0) cc_final: 0.8234 (pm20) REVERT: l 82 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6376 (ttp-170) REVERT: m 82 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.6922 (mmp-170) REVERT: o 66 THR cc_start: 0.8869 (m) cc_final: 0.8518 (m) REVERT: o 70 PHE cc_start: 0.9082 (t80) cc_final: 0.8810 (t80) REVERT: o 120 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.5282 (ptp-170) REVERT: p 30 LYS cc_start: 0.8643 (mttp) cc_final: 0.8343 (mmtm) REVERT: q 33 SER cc_start: 0.8895 (m) cc_final: 0.8335 (t) REVERT: s 38 MET cc_start: 0.7808 (tpp) cc_final: 0.7587 (tpp) REVERT: s 117 ARG cc_start: 0.7240 (tmm160) cc_final: 0.6782 (mpt-90) REVERT: y 31 ASP cc_start: 0.8888 (p0) cc_final: 0.8558 (p0) REVERT: 1 429 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7484 (tpp80) REVERT: 2 72 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7496 (mp) REVERT: 2 78 MET cc_start: 0.8919 (tpt) cc_final: 0.8506 (tpp) REVERT: 3 59 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8681 (mm) REVERT: 3 288 LYS cc_start: 0.7257 (tptp) cc_final: 0.7036 (tptp) REVERT: 6 76 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5996 (p90) REVERT: 9 36 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8030 (ttm) REVERT: e 37 GLU cc_start: 0.9213 (tp30) cc_final: 0.8951 (tp30) REVERT: f 34 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8330 (mp) REVERT: f 66 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7659 (ttpt) REVERT: f 67 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7453 (mm) outliers start: 216 outliers final: 114 residues processed: 929 average time/residue: 0.6651 time to fit residues: 1065.7008 Evaluate side-chains 862 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 733 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 71 GLU Chi-restraints excluded: chain 4 residue 144 ILE Chi-restraints excluded: chain 4 residue 145 THR Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 43 ILE Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 271 MET Chi-restraints excluded: chain M residue 405 LEU Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 250 SER Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 86 GLU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain k residue 107 GLN Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 144 ILE Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 69 GLN Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 62 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain o residue 120 ARG Chi-restraints excluded: chain p residue 78 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 30 PHE Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 116 ASP Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 91 THR Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 80 LEU Chi-restraints excluded: chain w residue 118 ILE Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain 1 residue 233 THR Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 1 residue 429 ARG Chi-restraints excluded: chain 2 residue 22 ASP Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 3 residue 248 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 420 ASP Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 61 HIS Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 86 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 156 LEU Chi-restraints excluded: chain 6 residue 157 LEU Chi-restraints excluded: chain 9 residue 36 MET Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 121 ASN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 327 LEU Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain f residue 34 LEU Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 80 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 10.0000 chunk 546 optimal weight: 8.9990 chunk 377 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 346 optimal weight: 30.0000 chunk 488 optimal weight: 8.9990 chunk 729 optimal weight: 10.0000 chunk 772 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 691 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 27 HIS ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN Y 63 ASN Y 105 GLN l 20 GLN 1 402 HIS ** 5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN e 24 GLN j 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68089 Z= 0.581 Angle : 1.566 50.894 92318 Z= 1.015 Chirality : 0.310 6.415 10124 Planarity : 0.004 0.062 11635 Dihedral : 6.606 169.597 9358 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.28 % Favored : 95.71 % Rotamer: Outliers : 4.29 % Allowed : 22.03 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 8082 helix: 1.20 (0.08), residues: 4171 sheet: -0.26 (0.26), residues: 421 loop : -0.66 (0.11), residues: 3490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP w 26 HIS 0.007 0.001 HIS H 304 PHE 0.026 0.001 PHE N 292 TYR 0.022 0.001 TYR z 43 ARG 0.004 0.000 ARG Y 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 756 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 71 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: 4 342 MET cc_start: 0.9013 (tpt) cc_final: 0.8630 (tpp) REVERT: A 44 MET cc_start: 0.5326 (mpp) cc_final: 0.4694 (tpt) REVERT: A 94 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8683 (tt) REVERT: L 28 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8334 (mmtm) REVERT: L 272 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.5454 (t80) REVERT: L 503 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4675 (tt0) REVERT: L 515 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.4069 (m-10) REVERT: L 571 MET cc_start: 0.8276 (mmt) cc_final: 0.7969 (mmt) REVERT: M 76 MET cc_start: 0.9132 (mtp) cc_final: 0.8909 (mtp) REVERT: M 395 LEU cc_start: 0.8660 (mt) cc_final: 0.8401 (mt) REVERT: M 458 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7918 (pp) REVERT: V 117 MET cc_start: 0.6850 (mpp) cc_final: 0.6374 (mpp) REVERT: X 71 MET cc_start: 0.8431 (mmt) cc_final: 0.8159 (mmm) REVERT: X 76 ILE cc_start: 0.9066 (mm) cc_final: 0.8758 (tt) REVERT: Y 67 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8382 (tp) REVERT: k 107 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7253 (tp40) REVERT: k 182 ARG cc_start: 0.6715 (tpp80) cc_final: 0.6445 (tpp80) REVERT: l 82 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6432 (ttp-170) REVERT: m 82 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.6814 (mmp-170) REVERT: o 120 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.5625 (ptp-170) REVERT: q 33 SER cc_start: 0.8895 (m) cc_final: 0.8406 (t) REVERT: s 117 ARG cc_start: 0.7193 (tmm160) cc_final: 0.6659 (mpt-90) REVERT: t 93 TYR cc_start: 0.7994 (m-80) cc_final: 0.7741 (m-10) REVERT: v 77 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: 1 107 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8553 (m-30) REVERT: 1 429 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7523 (tpp80) REVERT: 2 72 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7538 (mp) REVERT: 2 78 MET cc_start: 0.8952 (tpt) cc_final: 0.8531 (tpp) REVERT: 3 54 MET cc_start: 0.9385 (tpt) cc_final: 0.9134 (tpt) REVERT: 3 59 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8708 (mm) REVERT: 6 76 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5980 (p90) REVERT: 6 171 LYS cc_start: 0.8088 (tttm) cc_final: 0.7838 (tptm) REVERT: 9 36 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7992 (ttm) REVERT: e 37 GLU cc_start: 0.9195 (tp30) cc_final: 0.8931 (tp30) REVERT: f 34 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8519 (mp) REVERT: f 66 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7601 (ttpt) outliers start: 307 outliers final: 213 residues processed: 995 average time/residue: 0.6334 time to fit residues: 1103.2239 Evaluate side-chains 957 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 725 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 71 GLU Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 144 ILE Chi-restraints excluded: chain 4 residue 145 THR Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 43 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 396 ILE Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 503 GLU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 405 LEU Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain N residue 208 TYR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 250 SER Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain V residue 65 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 123 ASN Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 107 GLN Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 211 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 319 LEU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 61 ASP Chi-restraints excluded: chain l residue 69 GLN Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 62 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 27 THR Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain o residue 120 ARG Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 78 ASN Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 30 PHE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 26 LEU Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 116 ASP Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 91 THR Chi-restraints excluded: chain v residue 153 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 50 ASP Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 80 LEU Chi-restraints excluded: chain w residue 118 ILE Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain 1 residue 50 LEU Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 233 THR Chi-restraints excluded: chain 1 residue 253 THR Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 1 residue 429 ARG Chi-restraints excluded: chain 2 residue 22 ASP Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 37 ILE Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 248 MET Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 420 ASP Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 675 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 5 residue 45 PHE Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 59 MET Chi-restraints excluded: chain 6 residue 61 HIS Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 156 LEU Chi-restraints excluded: chain 6 residue 157 LEU Chi-restraints excluded: chain 6 residue 160 ILE Chi-restraints excluded: chain 9 residue 36 MET Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 138 GLU Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 243 GLN Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 327 LEU Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 34 LEU Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 34 LEU Chi-restraints excluded: chain g residue 92 THR Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 66 SER Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 81 MET Chi-restraints excluded: chain i residue 111 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 44 SER Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 80 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 5.9990 chunk 438 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 575 optimal weight: 7.9990 chunk 318 optimal weight: 20.0000 chunk 659 optimal weight: 10.0000 chunk 533 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 394 optimal weight: 40.0000 chunk 693 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 GLN Y 105 GLN l 20 GLN o 88 HIS ** 5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68089 Z= 0.588 Angle : 1.571 50.957 92318 Z= 1.017 Chirality : 0.310 6.428 10124 Planarity : 0.004 0.062 11635 Dihedral : 6.615 169.340 9358 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.26 % Favored : 95.73 % Rotamer: Outliers : 4.81 % Allowed : 22.27 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 8082 helix: 1.21 (0.08), residues: 4178 sheet: -0.30 (0.26), residues: 427 loop : -0.65 (0.11), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP w 26 HIS 0.008 0.001 HIS L 67 PHE 0.025 0.001 PHE N 292 TYR 0.023 0.001 TYR z 43 ARG 0.004 0.000 ARG t 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16164 Ramachandran restraints generated. 8082 Oldfield, 0 Emsley, 8082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 752 time to evaluate : 5.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 19 MET cc_start: 0.7084 (tpt) cc_final: 0.6643 (tpt) REVERT: 4 71 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6263 (mt-10) REVERT: 4 342 MET cc_start: 0.8985 (tpt) cc_final: 0.8423 (tpp) REVERT: A 44 MET cc_start: 0.5475 (mpp) cc_final: 0.4857 (tpt) REVERT: A 94 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8642 (tt) REVERT: L 28 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8224 (mmtm) REVERT: L 272 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5482 (t80) REVERT: L 366 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: L 503 GLU cc_start: 0.5352 (OUTLIER) cc_final: 0.4834 (tt0) REVERT: L 515 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.4066 (m-10) REVERT: L 571 MET cc_start: 0.8313 (mmt) cc_final: 0.7959 (mmt) REVERT: M 76 MET cc_start: 0.9121 (mtp) cc_final: 0.8880 (mtp) REVERT: M 458 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7954 (pp) REVERT: N 294 MET cc_start: 0.9209 (mmm) cc_final: 0.8980 (tpp) REVERT: V 117 MET cc_start: 0.6760 (mpp) cc_final: 0.6288 (mpp) REVERT: X 76 ILE cc_start: 0.9114 (mm) cc_final: 0.8804 (tt) REVERT: k 107 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7258 (tp40) REVERT: k 182 ARG cc_start: 0.6647 (tpp80) cc_final: 0.6443 (tpp80) REVERT: k 191 GLU cc_start: 0.8608 (pt0) cc_final: 0.8214 (pm20) REVERT: k 239 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: l 82 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6432 (ttp-170) REVERT: m 82 ARG cc_start: 0.7412 (mmt-90) cc_final: 0.6958 (mmp-170) REVERT: n 51 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6884 (mtt-85) REVERT: o 120 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.5590 (ptp-170) REVERT: p 30 LYS cc_start: 0.8724 (mttp) cc_final: 0.8380 (mmtm) REVERT: q 33 SER cc_start: 0.8844 (m) cc_final: 0.8391 (t) REVERT: s 117 ARG cc_start: 0.7010 (tmm160) cc_final: 0.6521 (mpt-90) REVERT: v 42 MET cc_start: 0.8605 (tpp) cc_final: 0.8217 (tpp) REVERT: v 77 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: 1 107 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: 1 409 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: 1 429 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7495 (tpp80) REVERT: 2 72 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7552 (mp) REVERT: 2 124 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7938 (tp) REVERT: 3 59 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8699 (mm) REVERT: 5 46 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8367 (p) REVERT: 6 76 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6031 (p90) REVERT: 6 178 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7601 (mmt90) REVERT: 9 36 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: e 37 GLU cc_start: 0.9140 (tp30) cc_final: 0.8889 (tp30) REVERT: f 66 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7619 (ttpt) REVERT: f 115 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6128 (pp) REVERT: g 60 ASP cc_start: 0.8708 (p0) cc_final: 0.7968 (m-30) outliers start: 344 outliers final: 248 residues processed: 1022 average time/residue: 0.6058 time to fit residues: 1080.6294 Evaluate side-chains 1004 residues out of total 7159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 731 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 71 GLU Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 144 ILE Chi-restraints excluded: chain 4 residue 145 THR Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 292 ASP Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 83 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 272 PHE Chi-restraints excluded: chain L residue 366 MET Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 503 GLU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 575 THR Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 405 LEU Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain N residue 208 TYR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 250 SER Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain V residue 65 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 88 ASN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 44 SER Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 39 LEU Chi-restraints excluded: chain Z residue 86 GLU Chi-restraints excluded: chain Z residue 123 ASN Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 107 GLN Chi-restraints excluded: chain k residue 122 VAL Chi-restraints excluded: chain k residue 195 THR Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 211 LEU Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 239 GLN Chi-restraints excluded: chain k residue 279 LEU Chi-restraints excluded: chain k residue 282 VAL Chi-restraints excluded: chain k residue 319 LEU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 69 GLN Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 62 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 51 ARG Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 27 THR Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain o residue 120 ARG Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 78 ASN Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 30 PHE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 34 ASP Chi-restraints excluded: chain t residue 72 HIS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 170 VAL Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 50 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 91 THR Chi-restraints excluded: chain v residue 153 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 50 ASP Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 80 LEU Chi-restraints excluded: chain w residue 118 ILE Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 233 THR Chi-restraints excluded: chain 1 residue 253 THR Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 365 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 429 ARG Chi-restraints excluded: chain 2 residue 72 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 2 residue 155 GLN Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 37 ILE Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 248 MET Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 420 ASP Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 540 ASP Chi-restraints excluded: chain 3 residue 583 THR Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 3 residue 668 ILE Chi-restraints excluded: chain 3 residue 675 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 5 residue 45 PHE Chi-restraints excluded: chain 5 residue 46 SER Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 58 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 LEU Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 59 MET Chi-restraints excluded: chain 6 residue 61 HIS Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 6 residue 156 LEU Chi-restraints excluded: chain 6 residue 157 LEU Chi-restraints excluded: chain 6 residue 160 ILE Chi-restraints excluded: chain 6 residue 178 ARG Chi-restraints excluded: chain 9 residue 36 MET Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 138 GLU Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 121 ASN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 105 ASP Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 154 LYS Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 243 GLN Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 327 LEU Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 61 GLU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 34 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 92 THR Chi-restraints excluded: chain g residue 93 ILE Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 66 SER Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 81 MET Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 111 THR Chi-restraints excluded: chain i residue 129 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 44 SER Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 MET Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 80 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 20.0000 chunk 695 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 773 optimal weight: 8.9990 chunk 641 optimal weight: 9.9990 chunk 357 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 405 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: