Starting phenix.real_space_refine on Wed Feb 14 10:19:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6s_10104/02_2024/6s6s_10104_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 44 7.16 5 P 12 5.49 5 S 356 5.16 5 C 37508 2.51 5 N 10796 2.21 5 O 11328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A ASP 973": "OD1" <-> "OD2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A ASP 1078": "OD1" <-> "OD2" Residue "A ASP 1182": "OD1" <-> "OD2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A GLU 1287": "OE1" <-> "OE2" Residue "A ASP 1291": "OD1" <-> "OD2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A GLU 1429": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B ARG 782": "NH1" <-> "NH2" Residue "B GLU 844": "OE1" <-> "OE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 978": "OE1" <-> "OE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 993": "OD1" <-> "OD2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "B GLU 1148": "OE1" <-> "OE2" Residue "B ASP 1182": "OD1" <-> "OD2" Residue "B TYR 1367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1446": "OD1" <-> "OD2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C GLU 951": "OE1" <-> "OE2" Residue "C PHE 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "C ASP 1180": "OD1" <-> "OD2" Residue "C GLU 1408": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D GLU 726": "OE1" <-> "OE2" Residue "D ARG 782": "NH1" <-> "NH2" Residue "D GLU 927": "OE1" <-> "OE2" Residue "D ASP 1166": "OD1" <-> "OD2" Residue "D GLU 1194": "OE1" <-> "OE2" Residue "D GLU 1206": "OE1" <-> "OE2" Residue "D ASP 1212": "OD1" <-> "OD2" Residue "D GLU 1287": "OE1" <-> "OE2" Residue "D ASP 1291": "OD1" <-> "OD2" Residue "D GLU 1358": "OE1" <-> "OE2" Residue "D ASP 1398": "OD1" <-> "OD2" Residue "D GLU 1429": "OE1" <-> "OE2" Residue "D GLU 1434": "OE1" <-> "OE2" Residue "D GLU 1467": "OE1" <-> "OE2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "G ASP 68": "OD1" <-> "OD2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G GLU 403": "OE1" <-> "OE2" Residue "G ASP 406": "OD1" <-> "OD2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 429": "NH1" <-> "NH2" Residue "G ASP 460": "OD1" <-> "OD2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E GLU 405": "OE1" <-> "OE2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 429": "NH1" <-> "NH2" Residue "E ASP 443": "OD1" <-> "OD2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ASP 264": "OD1" <-> "OD2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "H PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H ARG 145": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ASP 210": "OD1" <-> "OD2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H GLU 344": "OE1" <-> "OE2" Residue "H PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 367": "NH1" <-> "NH2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 403": "OE1" <-> "OE2" Residue "H ASP 406": "OD1" <-> "OD2" Residue "H ASP 412": "OD1" <-> "OD2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H GLU 474": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 60044 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 11311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1468, 11311 Classifications: {'peptide': 1468} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1406} Chain breaks: 1 Chain: "B" Number of atoms: 11311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1468, 11311 Classifications: {'peptide': 1468} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1406} Chain breaks: 1 Chain: "C" Number of atoms: 11311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1468, 11311 Classifications: {'peptide': 1468} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1406} Chain breaks: 1 Chain: "D" Number of atoms: 11311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1468, 11311 Classifications: {'peptide': 1468} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1406} Chain breaks: 1 Chain: "G" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 20, 'TRANS': 449} Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 20, 'TRANS': 449} Chain: "F" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 20, 'TRANS': 449} Chain: "H" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 20, 'TRANS': 449} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8559 SG CYS A1113 50.012 83.792 106.542 1.00 73.07 S ATOM 8473 SG CYS A1102 55.015 81.308 108.645 1.00 79.50 S ATOM 8522 SG CYS A1108 52.811 82.542 103.092 1.00 78.57 S ATOM 19870 SG CYS B1113 81.262 148.952 70.413 1.00 48.88 S ATOM 19784 SG CYS B1102 85.210 144.855 69.101 1.00 48.17 S ATOM 19833 SG CYS B1108 86.844 150.444 72.145 1.00 48.61 S ATOM 31181 SG CYS C1113 157.048 57.037 68.106 1.00 48.48 S ATOM 31095 SG CYS C1102 153.601 60.934 67.507 1.00 50.18 S ATOM 31144 SG CYS C1108 152.697 55.566 69.559 1.00 52.80 S ATOM 42492 SG CYS D1113 189.396 120.011 107.231 1.00 73.81 S ATOM 42406 SG CYS D1102 184.167 123.205 109.064 1.00 71.98 S ATOM 42455 SG CYS D1108 186.018 121.815 103.389 1.00 67.74 S ATOM 45620 SG CYS G 51 45.281 74.696 108.316 1.00 97.45 S ATOM 45655 SG CYS G 56 42.088 71.311 111.604 1.00 97.21 S ATOM 45599 SG CYS G 48 39.578 74.409 106.918 1.00 98.66 S ATOM 45655 SG CYS G 56 42.088 71.311 111.604 1.00 97.21 S ATOM 46070 SG CYS G 109 41.357 75.614 112.618 1.00 93.25 S ATOM 46043 SG CYS G 105 38.449 67.963 117.333 1.00108.70 S ATOM 45687 SG CYS G 60 39.702 64.200 116.599 1.00105.88 S ATOM 45994 SG CYS G 99 35.720 64.956 120.695 1.00131.38 S ATOM 49192 SG CYS E 48 79.755 155.720 58.552 1.00 59.35 S ATOM 49213 SG CYS E 51 82.002 151.371 59.601 1.00 52.63 S ATOM 49248 SG CYS E 56 81.721 151.669 54.705 1.00 53.30 S ATOM 49192 SG CYS E 48 79.755 155.720 58.552 1.00 59.35 S ATOM 49663 SG CYS E 109 76.896 151.313 57.876 1.00 57.06 S ATOM 49636 SG CYS E 105 75.738 150.037 48.962 1.00 66.37 S ATOM 49280 SG CYS E 60 81.148 149.542 46.269 1.00 55.18 S ATOM 49587 SG CYS E 99 74.689 149.495 44.063 1.00 67.56 S ATOM 52785 SG CYS F 48 159.722 50.765 55.868 1.00 56.48 S ATOM 52806 SG CYS F 51 156.984 54.979 57.218 1.00 50.89 S ATOM 52841 SG CYS F 56 157.430 55.281 52.450 1.00 49.73 S ATOM 52785 SG CYS F 48 159.722 50.765 55.868 1.00 56.48 S ATOM 53256 SG CYS F 109 161.937 55.203 55.411 1.00 53.01 S ATOM 53229 SG CYS F 105 162.668 57.258 46.463 1.00 63.20 S ATOM 52873 SG CYS F 60 157.698 57.718 44.259 1.00 55.74 S ATOM 53180 SG CYS F 99 162.790 58.342 40.631 1.00 68.23 S ATOM 56399 SG CYS H 51 194.390 129.398 108.475 1.00 80.21 S ATOM 56434 SG CYS H 56 197.282 133.845 112.204 1.00 88.60 S ATOM 56378 SG CYS H 48 199.638 130.419 107.270 1.00 82.60 S ATOM 56849 SG CYS H 109 198.775 128.216 113.331 1.00 84.66 S ATOM 56822 SG CYS H 105 202.739 134.609 118.570 1.00110.76 S ATOM 56466 SG CYS H 60 199.473 140.115 117.314 1.00 96.51 S ATOM 56773 SG CYS H 99 204.507 139.854 121.220 1.00119.85 S Time building chain proxies: 22.96, per 1000 atoms: 0.38 Number of scatterers: 60044 At special positions: 0 Unit cell: (240.994, 205.344, 172.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 44 26.01 S 356 16.00 P 12 15.00 O 11328 8.00 N 10796 7.00 C 37508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 18.60 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A1502 " pdb="FE1 F3S A1502 " - pdb=" SG CYS A1113 " pdb="FE3 F3S A1502 " - pdb=" SG CYS A1102 " pdb="FE4 F3S A1502 " - pdb=" SG CYS A1108 " pdb=" F3S B1502 " pdb="FE1 F3S B1502 " - pdb=" SG CYS B1113 " pdb="FE3 F3S B1502 " - pdb=" SG CYS B1102 " pdb="FE4 F3S B1502 " - pdb=" SG CYS B1108 " pdb=" F3S C1502 " pdb="FE1 F3S C1502 " - pdb=" SG CYS C1113 " pdb="FE4 F3S C1502 " - pdb=" SG CYS C1108 " pdb="FE3 F3S C1502 " - pdb=" SG CYS C1102 " pdb=" F3S D1502 " pdb="FE3 F3S D1502 " - pdb=" SG CYS D1102 " pdb="FE1 F3S D1502 " - pdb=" SG CYS D1113 " pdb="FE4 F3S D1502 " - pdb=" SG CYS D1108 " pdb=" SF4 E 501 " pdb="FE1 SF4 E 501 " - pdb=" SG CYS E 51 " pdb="FE2 SF4 E 501 " - pdb=" SG CYS E 56 " pdb="FE3 SF4 E 501 " - pdb=" SG CYS E 48 " pdb="FE4 SF4 E 501 " - pdb=" SG CYS E 109 " pdb=" SF4 E 502 " pdb="FE1 SF4 E 502 " - pdb=" SG CYS E 105 " pdb="FE2 SF4 E 502 " - pdb=" SG CYS E 60 " pdb="FE4 SF4 E 502 " - pdb=" SG CYS E 99 " pdb=" SF4 F 501 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 109 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 56 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 48 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 51 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 60 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 105 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 99 " pdb=" SF4 G 501 " pdb="FE2 SF4 G 501 " - pdb=" SG CYS G 56 " pdb="FE4 SF4 G 501 " - pdb=" SG CYS G 109 " pdb="FE3 SF4 G 501 " - pdb=" SG CYS G 48 " pdb="FE1 SF4 G 501 " - pdb=" SG CYS G 51 " pdb=" SF4 G 502 " pdb="FE1 SF4 G 502 " - pdb=" SG CYS G 105 " pdb="FE2 SF4 G 502 " - pdb=" SG CYS G 60 " pdb="FE4 SF4 G 502 " - pdb=" SG CYS G 99 " pdb=" SF4 H 501 " pdb="FE2 SF4 H 501 " - pdb=" SG CYS H 56 " pdb="FE4 SF4 H 501 " - pdb=" SG CYS H 109 " pdb="FE3 SF4 H 501 " - pdb=" SG CYS H 48 " pdb="FE1 SF4 H 501 " - pdb=" SG CYS H 51 " pdb=" SF4 H 502 " pdb="FE2 SF4 H 502 " - pdb=" SG CYS H 60 " pdb="FE1 SF4 H 502 " - pdb=" SG CYS H 105 " pdb="FE4 SF4 H 502 " - pdb=" SG CYS H 99 " Number of angles added : 120 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 60 sheets defined 35.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.793A pdb=" N ALA A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 141 through 162 removed outlier: 4.103A pdb=" N GLU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 4.474A pdb=" N THR A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 238 through 249 removed outlier: 4.761A pdb=" N THR A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.864A pdb=" N GLN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.849A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Proline residue: A 467 - end of helix removed outlier: 3.955A pdb=" N ASP A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 552 through 565 removed outlier: 6.202A pdb=" N ASP A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 669 through 680 Processing helix chain 'A' and resid 689 through 711 removed outlier: 4.399A pdb=" N MET A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 807 through 819 Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.361A pdb=" N ARG A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 1006 through 1015 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1045 through 1058 Processing helix chain 'A' and resid 1062 through 1064 No H-bonds generated for 'chain 'A' and resid 1062 through 1064' Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1093 through 1100 Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.522A pdb=" N GLN A1126 " --> pdb=" O ASP A1122 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1127' Processing helix chain 'A' and resid 1132 through 1153 Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1211 through 1218 removed outlier: 3.589A pdb=" N ASP A1218 " --> pdb=" O ARG A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 Processing helix chain 'A' and resid 1245 through 1254 Processing helix chain 'A' and resid 1317 through 1319 No H-bonds generated for 'chain 'A' and resid 1317 through 1319' Processing helix chain 'A' and resid 1401 through 1404 No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1418 through 1435 Processing helix chain 'A' and resid 1438 through 1445 Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.800A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 84 through 100 removed outlier: 4.288A pdb=" N PHE B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 141 through 162 removed outlier: 3.583A pdb=" N GLU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.986A pdb=" N THR B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.719A pdb=" N THR B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.778A pdb=" N ALA B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 403 through 413 removed outlier: 3.929A pdb=" N LEU B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 428 through 434 removed outlier: 3.561A pdb=" N ALA B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 495 through 498 Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 552 through 565 removed outlier: 6.709A pdb=" N ASP B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B 565 " --> pdb=" O TYR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 598 Processing helix chain 'B' and resid 620 through 633 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 652 through 660 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.896A pdb=" N ARG B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 removed outlier: 4.328A pdb=" N MET B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 719 No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 807 through 818 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 846 through 850 Processing helix chain 'B' and resid 865 through 878 Processing helix chain 'B' and resid 891 through 893 No H-bonds generated for 'chain 'B' and resid 891 through 893' Processing helix chain 'B' and resid 951 through 957 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 1007 through 1015 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1045 through 1058 Processing helix chain 'B' and resid 1062 through 1064 No H-bonds generated for 'chain 'B' and resid 1062 through 1064' Processing helix chain 'B' and resid 1076 through 1085 Processing helix chain 'B' and resid 1093 through 1100 Processing helix chain 'B' and resid 1122 through 1127 removed outlier: 3.979A pdb=" N LYS B1127 " --> pdb=" O LYS B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1153 removed outlier: 3.904A pdb=" N VAL B1136 " --> pdb=" O PRO B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1160 No H-bonds generated for 'chain 'B' and resid 1158 through 1160' Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1184 through 1187 No H-bonds generated for 'chain 'B' and resid 1184 through 1187' Processing helix chain 'B' and resid 1211 through 1225 removed outlier: 3.719A pdb=" N ASP B1218 " --> pdb=" O ARG B1214 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG B1220 " --> pdb=" O VAL B1216 " (cutoff:3.500A) Proline residue: B1221 - end of helix Processing helix chain 'B' and resid 1245 through 1253 Processing helix chain 'B' and resid 1317 through 1319 No H-bonds generated for 'chain 'B' and resid 1317 through 1319' Processing helix chain 'B' and resid 1401 through 1404 No H-bonds generated for 'chain 'B' and resid 1401 through 1404' Processing helix chain 'B' and resid 1418 through 1435 Processing helix chain 'B' and resid 1438 through 1453 removed outlier: 3.847A pdb=" N ASP B1446 " --> pdb=" O GLU B1442 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP B1447 " --> pdb=" O ILE B1443 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B1448 " --> pdb=" O LEU B1444 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG B1449 " --> pdb=" O ASN B1445 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR B1452 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B1453 " --> pdb=" O ARG B1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.804A pdb=" N ALA C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 84 through 100 removed outlier: 3.957A pdb=" N ALA C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.653A pdb=" N GLU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 238 through 249 removed outlier: 4.696A pdb=" N THR C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 403 through 413 removed outlier: 4.219A pdb=" N LEU C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.375A pdb=" N GLN C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN C 422 " --> pdb=" O LYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 458 through 470 removed outlier: 4.271A pdb=" N HIS C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 552 through 562 Processing helix chain 'C' and resid 581 through 598 Processing helix chain 'C' and resid 620 through 633 Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 669 through 681 removed outlier: 3.596A pdb=" N ARG C 681 " --> pdb=" O GLU C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 removed outlier: 4.388A pdb=" N MET C 711 " --> pdb=" O ILE C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 719 No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 751 through 766 Processing helix chain 'C' and resid 792 through 804 Processing helix chain 'C' and resid 807 through 817 Processing helix chain 'C' and resid 826 through 828 No H-bonds generated for 'chain 'C' and resid 826 through 828' Processing helix chain 'C' and resid 846 through 852 removed outlier: 4.534A pdb=" N ARG C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 878 Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' Processing helix chain 'C' and resid 921 through 923 No H-bonds generated for 'chain 'C' and resid 921 through 923' Processing helix chain 'C' and resid 951 through 957 Processing helix chain 'C' and resid 977 through 990 Processing helix chain 'C' and resid 1006 through 1015 Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'C' and resid 1045 through 1058 Processing helix chain 'C' and resid 1062 through 1064 No H-bonds generated for 'chain 'C' and resid 1062 through 1064' Processing helix chain 'C' and resid 1076 through 1085 Processing helix chain 'C' and resid 1094 through 1100 Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1132 through 1153 Processing helix chain 'C' and resid 1158 through 1160 No H-bonds generated for 'chain 'C' and resid 1158 through 1160' Processing helix chain 'C' and resid 1184 through 1187 No H-bonds generated for 'chain 'C' and resid 1184 through 1187' Processing helix chain 'C' and resid 1212 through 1217 Processing helix chain 'C' and resid 1219 through 1224 Processing helix chain 'C' and resid 1244 through 1253 Processing helix chain 'C' and resid 1401 through 1403 No H-bonds generated for 'chain 'C' and resid 1401 through 1403' Processing helix chain 'C' and resid 1418 through 1435 Processing helix chain 'C' and resid 1438 through 1452 removed outlier: 3.849A pdb=" N ASP C1446 " --> pdb=" O GLU C1442 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP C1447 " --> pdb=" O ILE C1443 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C1448 " --> pdb=" O LEU C1444 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG C1449 " --> pdb=" O ASN C1445 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THR C1452 " --> pdb=" O ALA C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1460 through 1465 removed outlier: 3.759A pdb=" N LEU C1463 " --> pdb=" O LYS C1460 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN C1464 " --> pdb=" O GLU C1461 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C1465 " --> pdb=" O MET C1462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1460 through 1465' Processing helix chain 'D' and resid 16 through 27 removed outlier: 4.048A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.363A pdb=" N THR D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 162 removed outlier: 3.610A pdb=" N GLU D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 238 through 250 removed outlier: 4.458A pdb=" N THR D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.650A pdb=" N THR D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.816A pdb=" N VAL D 420 " --> pdb=" O TRP D 416 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 422' Processing helix chain 'D' and resid 428 through 434 removed outlier: 3.599A pdb=" N ALA D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 454 removed outlier: 3.861A pdb=" N PHE D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.832A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 552 through 562 Processing helix chain 'D' and resid 581 through 599 Processing helix chain 'D' and resid 620 through 633 Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 670 through 679 Processing helix chain 'D' and resid 689 through 709 Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 751 through 766 Processing helix chain 'D' and resid 792 through 804 Processing helix chain 'D' and resid 807 through 817 Processing helix chain 'D' and resid 825 through 828 Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 847 through 852 removed outlier: 4.544A pdb=" N ARG D 852 " --> pdb=" O ALA D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 878 Processing helix chain 'D' and resid 891 through 893 No H-bonds generated for 'chain 'D' and resid 891 through 893' Processing helix chain 'D' and resid 919 through 922 No H-bonds generated for 'chain 'D' and resid 919 through 922' Processing helix chain 'D' and resid 951 through 956 Processing helix chain 'D' and resid 977 through 990 Processing helix chain 'D' and resid 1006 through 1015 Processing helix chain 'D' and resid 1035 through 1039 Processing helix chain 'D' and resid 1045 through 1058 Processing helix chain 'D' and resid 1062 through 1064 No H-bonds generated for 'chain 'D' and resid 1062 through 1064' Processing helix chain 'D' and resid 1076 through 1085 Processing helix chain 'D' and resid 1095 through 1098 No H-bonds generated for 'chain 'D' and resid 1095 through 1098' Processing helix chain 'D' and resid 1108 through 1110 No H-bonds generated for 'chain 'D' and resid 1108 through 1110' Processing helix chain 'D' and resid 1122 through 1127 removed outlier: 3.922A pdb=" N LYS D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1153 removed outlier: 3.648A pdb=" N VAL D1136 " --> pdb=" O PRO D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1160 No H-bonds generated for 'chain 'D' and resid 1158 through 1160' Processing helix chain 'D' and resid 1183 through 1187 removed outlier: 3.671A pdb=" N LEU D1187 " --> pdb=" O ASN D1184 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1222 through 1225 No H-bonds generated for 'chain 'D' and resid 1222 through 1225' Processing helix chain 'D' and resid 1244 through 1254 Processing helix chain 'D' and resid 1401 through 1403 No H-bonds generated for 'chain 'D' and resid 1401 through 1403' Processing helix chain 'D' and resid 1418 through 1435 Processing helix chain 'D' and resid 1438 through 1450 removed outlier: 3.642A pdb=" N ASP D1446 " --> pdb=" O GLU D1442 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA D1448 " --> pdb=" O LEU D1444 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG D1449 " --> pdb=" O ASN D1445 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 66 through 75 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 92 through 98 removed outlier: 4.284A pdb=" N ARG G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.939A pdb=" N ALA G 132 " --> pdb=" O ILE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 262 through 274 removed outlier: 4.593A pdb=" N SER G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 300 through 311 Processing helix chain 'G' and resid 332 through 341 Processing helix chain 'G' and resid 407 through 410 No H-bonds generated for 'chain 'G' and resid 407 through 410' Processing helix chain 'G' and resid 442 through 444 No H-bonds generated for 'chain 'G' and resid 442 through 444' Processing helix chain 'G' and resid 452 through 473 Processing helix chain 'E' and resid 22 through 25 No H-bonds generated for 'chain 'E' and resid 22 through 25' Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.791A pdb=" N ASN E 46 " --> pdb=" O ASN E 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 92 through 98 removed outlier: 3.829A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 121 through 135 removed outlier: 3.762A pdb=" N ALA E 132 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 170 Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 262 through 274 removed outlier: 5.034A pdb=" N SER E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 311 Processing helix chain 'E' and resid 332 through 341 Processing helix chain 'E' and resid 407 through 410 No H-bonds generated for 'chain 'E' and resid 407 through 410' Processing helix chain 'E' and resid 443 through 446 No H-bonds generated for 'chain 'E' and resid 443 through 446' Processing helix chain 'E' and resid 451 through 474 Processing helix chain 'F' and resid 22 through 25 No H-bonds generated for 'chain 'F' and resid 22 through 25' Processing helix chain 'F' and resid 38 through 47 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 110 through 113 No H-bonds generated for 'chain 'F' and resid 110 through 113' Processing helix chain 'F' and resid 121 through 135 removed outlier: 3.522A pdb=" N ALA F 132 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 198 through 211 removed outlier: 4.005A pdb=" N GLU F 202 " --> pdb=" O LYS F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 262 through 275 removed outlier: 5.100A pdb=" N SER F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 443 through 446 No H-bonds generated for 'chain 'F' and resid 443 through 446' Processing helix chain 'F' and resid 451 through 473 Processing helix chain 'H' and resid 22 through 25 No H-bonds generated for 'chain 'H' and resid 22 through 25' Processing helix chain 'H' and resid 38 through 44 removed outlier: 3.620A pdb=" N ASN H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.811A pdb=" N HIS H 59 " --> pdb=" O CYS H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.974A pdb=" N SER H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 removed outlier: 3.641A pdb=" N VAL H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 removed outlier: 3.893A pdb=" N ARG H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 113 No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.642A pdb=" N ALA H 132 " --> pdb=" O ILE H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 170 removed outlier: 3.809A pdb=" N ALA H 169 " --> pdb=" O GLU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 187 No H-bonds generated for 'chain 'H' and resid 185 through 187' Processing helix chain 'H' and resid 198 through 211 Processing helix chain 'H' and resid 227 through 233 removed outlier: 3.528A pdb=" N ARG H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 270 removed outlier: 3.503A pdb=" N SER H 269 " --> pdb=" O TYR H 265 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 275 No H-bonds generated for 'chain 'H' and resid 272 through 275' Processing helix chain 'H' and resid 280 through 283 No H-bonds generated for 'chain 'H' and resid 280 through 283' Processing helix chain 'H' and resid 300 through 311 removed outlier: 3.712A pdb=" N ARG H 311 " --> pdb=" O ARG H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 removed outlier: 3.696A pdb=" N ALA H 336 " --> pdb=" O GLN H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 411 removed outlier: 3.521A pdb=" N PHE H 411 " --> pdb=" O LEU H 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 407 through 411' Processing helix chain 'H' and resid 442 through 444 No H-bonds generated for 'chain 'H' and resid 442 through 444' Processing helix chain 'H' and resid 451 through 474 removed outlier: 3.757A pdb=" N ARG H 456 " --> pdb=" O VAL H 452 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 470 " --> pdb=" O HIS H 466 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 354 through 357 removed outlier: 8.020A pdb=" N PHE A 204 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 49 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.902A pdb=" N GLN A 75 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 172 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 73 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 106 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 134 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE A 104 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 230 through 234 removed outlier: 3.726A pdb=" N ASN A 231 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 499 through 501 Processing sheet with id= E, first strand: chain 'A' and resid 524 through 526 Processing sheet with id= F, first strand: chain 'A' and resid 566 through 569 removed outlier: 7.035A pdb=" N HIS A 603 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE A 569 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 605 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 641 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 606 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 643 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR A 665 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR A 646 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN A 667 " --> pdb=" O THR A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 572 through 574 Processing sheet with id= H, first strand: chain 'A' and resid 829 through 831 Processing sheet with id= I, first strand: chain 'A' and resid 907 through 909 removed outlier: 6.853A pdb=" N GLU A 927 " --> pdb=" O LYS A 908 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 997 through 1001 removed outlier: 6.283A pdb=" N ILE A1020 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A1000 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A1022 " --> pdb=" O LEU A1000 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 1068 through 1070 removed outlier: 6.313A pdb=" N GLU A1089 " --> pdb=" O THR A1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 1229 through 1235 removed outlier: 3.592A pdb=" N ASP A1291 " --> pdb=" O GLY A1270 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A1335 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VAL A1307 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE A1337 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A1354 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A1372 " --> pdb=" O VAL A1355 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A1357 " --> pdb=" O THR A1372 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A1374 " --> pdb=" O VAL A1357 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 379 through 384 removed outlier: 7.027A pdb=" N ILE B 357 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS B 382 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR B 355 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE B 204 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA B 49 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.806A pdb=" N GLN B 75 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 172 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 73 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 106 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.707A pdb=" N ASN B 231 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 499 through 501 Processing sheet with id= Q, first strand: chain 'B' and resid 524 through 526 Processing sheet with id= R, first strand: chain 'B' and resid 568 through 570 removed outlier: 7.855A pdb=" N ILE B 569 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 605 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER B 641 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 606 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 643 " --> pdb=" O LEU B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 572 through 574 Processing sheet with id= T, first strand: chain 'B' and resid 829 through 831 Processing sheet with id= U, first strand: chain 'B' and resid 907 through 910 removed outlier: 6.658A pdb=" N GLU B 927 " --> pdb=" O LYS B 908 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL B 910 " --> pdb=" O GLU B 927 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU B 929 " --> pdb=" O VAL B 910 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 1020 through 1024 removed outlier: 6.264A pdb=" N ARG B1066 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE B1023 " --> pdb=" O ARG B1066 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B1068 " --> pdb=" O ILE B1023 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU B1089 " --> pdb=" O THR B1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'B' and resid 1229 through 1235 removed outlier: 3.767A pdb=" N ASP B1291 " --> pdb=" O GLY B1270 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLY B1302 " --> pdb=" O ILE B1284 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N LEU B1286 " --> pdb=" O GLY B1302 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B1304 " --> pdb=" O LEU B1286 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL B1288 " --> pdb=" O THR B1304 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B1306 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY B1290 " --> pdb=" O VAL B1306 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG B1308 " --> pdb=" O GLY B1290 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA B1292 " --> pdb=" O ARG B1308 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA B1333 " --> pdb=" O GLY B1302 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B1304 " --> pdb=" O ALA B1333 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B1335 " --> pdb=" O THR B1304 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B1306 " --> pdb=" O LYS B1335 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE B1337 " --> pdb=" O VAL B1306 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG B1308 " --> pdb=" O PHE B1337 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B1354 " --> pdb=" O LEU B1336 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B1372 " --> pdb=" O VAL B1355 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B1357 " --> pdb=" O THR B1372 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B1374 " --> pdb=" O VAL B1357 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET B1391 " --> pdb=" O ALA B1373 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B1375 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B1393 " --> pdb=" O ILE B1375 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 379 through 384 removed outlier: 6.876A pdb=" N ILE C 357 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS C 382 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR C 355 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE C 204 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 49 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.820A pdb=" N GLN C 75 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU C 172 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 73 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 106 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY C 134 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE C 104 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 332 through 336 Processing sheet with id= AA, first strand: chain 'C' and resid 499 through 501 Processing sheet with id= AB, first strand: chain 'C' and resid 524 through 526 Processing sheet with id= AC, first strand: chain 'C' and resid 566 through 570 removed outlier: 6.273A pdb=" N HIS C 603 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE C 569 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 605 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER C 641 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU C 606 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN C 643 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR C 665 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR C 646 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN C 667 " --> pdb=" O THR C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'C' and resid 572 through 574 Processing sheet with id= AE, first strand: chain 'C' and resid 829 through 831 Processing sheet with id= AF, first strand: chain 'C' and resid 997 through 1001 removed outlier: 6.622A pdb=" N ILE C1020 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU C1000 " --> pdb=" O ILE C1020 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU C1022 " --> pdb=" O LEU C1000 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'C' and resid 1068 through 1070 removed outlier: 6.839A pdb=" N GLU C1089 " --> pdb=" O THR C1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'C' and resid 1229 through 1235 removed outlier: 3.984A pdb=" N ASP C1291 " --> pdb=" O GLY C1270 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C1304 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C1288 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C1306 " --> pdb=" O VAL C1288 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLY C1290 " --> pdb=" O VAL C1306 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG C1308 " --> pdb=" O GLY C1290 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA C1292 " --> pdb=" O ARG C1308 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS C1335 " --> pdb=" O ILE C1305 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL C1307 " --> pdb=" O LYS C1335 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE C1337 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR C1354 " --> pdb=" O LEU C1336 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA C1338 " --> pdb=" O THR C1354 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C1356 " --> pdb=" O ALA C1338 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C1372 " --> pdb=" O VAL C1355 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C1357 " --> pdb=" O THR C1372 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL C1374 " --> pdb=" O VAL C1357 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C1393 " --> pdb=" O ALA C1373 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 379 through 382 removed outlier: 7.067A pdb=" N ILE D 357 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS D 382 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR D 355 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE D 204 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 49 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.905A pdb=" N GLN D 75 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU D 172 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 73 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY D 106 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY D 134 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE D 104 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 332 through 336 Processing sheet with id= AL, first strand: chain 'D' and resid 499 through 501 Processing sheet with id= AM, first strand: chain 'D' and resid 524 through 526 Processing sheet with id= AN, first strand: chain 'D' and resid 566 through 570 removed outlier: 6.751A pdb=" N HIS D 603 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE D 569 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 605 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER D 641 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU D 606 " --> pdb=" O SER D 641 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 643 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 665 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR D 646 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN D 667 " --> pdb=" O THR D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'D' and resid 572 through 574 Processing sheet with id= AP, first strand: chain 'D' and resid 829 through 831 Processing sheet with id= AQ, first strand: chain 'D' and resid 927 through 931 removed outlier: 6.191A pdb=" N LYS D 995 " --> pdb=" O LEU D 928 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE D 930 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 997 " --> pdb=" O ILE D 930 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D1020 " --> pdb=" O VAL D 998 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU D1000 " --> pdb=" O ILE D1020 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D1022 " --> pdb=" O LEU D1000 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG D1066 " --> pdb=" O ILE D1021 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE D1023 " --> pdb=" O ARG D1066 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D1068 " --> pdb=" O ILE D1023 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU D1089 " --> pdb=" O THR D1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'D' and resid 1229 through 1235 removed outlier: 3.544A pdb=" N ASP D1291 " --> pdb=" O GLY D1270 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR D1304 " --> pdb=" O LEU D1286 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL D1288 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL D1306 " --> pdb=" O VAL D1288 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY D1290 " --> pdb=" O VAL D1306 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG D1308 " --> pdb=" O GLY D1290 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS D1335 " --> pdb=" O ILE D1305 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL D1307 " --> pdb=" O LYS D1335 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D1337 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D1372 " --> pdb=" O VAL D1355 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL D1357 " --> pdb=" O THR D1372 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D1374 " --> pdb=" O VAL D1357 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET D1391 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ILE D1375 " --> pdb=" O MET D1391 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR D1393 " --> pdb=" O ILE D1375 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 438 through 440 removed outlier: 6.266A pdb=" N VAL G 237 " --> pdb=" O PHE G 439 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LEU G 238 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY G 152 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU G 173 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL G 153 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE G 214 " --> pdb=" O VAL G 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'G' and resid 259 through 261 removed outlier: 7.355A pdb=" N VAL G 396 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 294 " --> pdb=" O ILE G 397 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA G 399 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 296 " --> pdb=" O ALA G 399 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS G 318 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLY G 297 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU G 320 " --> pdb=" O GLY G 297 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'G' and resid 389 through 392 removed outlier: 6.384A pdb=" N VAL G 366 " --> pdb=" O PRO G 351 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 368 through 370 Processing sheet with id= AW, first strand: chain 'E' and resid 438 through 440 removed outlier: 6.062A pdb=" N VAL E 237 " --> pdb=" O PHE E 439 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 214 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 395 through 397 removed outlier: 7.473A pdb=" N GLU E 344 " --> pdb=" O CYS E 319 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 388 through 392 removed outlier: 5.926A pdb=" N VAL E 366 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 368 through 370 Processing sheet with id= BA, first strand: chain 'F' and resid 438 through 440 removed outlier: 6.661A pdb=" N VAL F 237 " --> pdb=" O PHE F 439 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA F 236 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU F 173 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL F 153 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS F 175 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE F 214 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.523A pdb=" N VAL F 396 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 294 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU F 344 " --> pdb=" O CYS F 319 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR F 321 " --> pdb=" O GLU F 344 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE F 346 " --> pdb=" O TYR F 321 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.329A pdb=" N VAL F 366 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 368 through 370 Processing sheet with id= BE, first strand: chain 'H' and resid 438 through 440 removed outlier: 5.617A pdb=" N VAL H 237 " --> pdb=" O PHE H 439 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N LEU H 238 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY H 152 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU H 173 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL H 153 " --> pdb=" O GLU H 173 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE H 214 " --> pdb=" O VAL H 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'H' and resid 293 through 295 removed outlier: 6.487A pdb=" N LEU H 395 " --> pdb=" O VAL H 294 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'H' and resid 388 through 392 removed outlier: 3.998A pdb=" N GLY H 362 " --> pdb=" O THR H 355 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR H 355 " --> pdb=" O GLY H 362 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG H 364 " --> pdb=" O GLY H 353 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY H 353 " --> pdb=" O ARG H 364 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL H 366 " --> pdb=" O PRO H 351 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'H' and resid 368 through 370 1903 hydrogen bonds defined for protein. 5463 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: 25.75 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.77: 60552 1.77 - 2.32: 644 2.32 - 2.86: 0 2.86 - 3.41: 0 3.41 - 3.96: 12 Bond restraints: 61208 Sorted by residual: bond pdb=" S4 F3S B1502 " pdb="FE1 F3S B1502 " ideal model delta sigma weight residual 2.233 3.957 -1.724 2.00e-02 2.50e+03 7.43e+03 bond pdb=" S4 F3S C1502 " pdb="FE1 F3S C1502 " ideal model delta sigma weight residual 2.233 3.949 -1.716 2.00e-02 2.50e+03 7.36e+03 bond pdb=" S4 F3S A1502 " pdb="FE1 F3S A1502 " ideal model delta sigma weight residual 2.233 3.944 -1.711 2.00e-02 2.50e+03 7.32e+03 bond pdb=" S4 F3S D1502 " pdb="FE1 F3S D1502 " ideal model delta sigma weight residual 2.233 3.941 -1.708 2.00e-02 2.50e+03 7.29e+03 bond pdb=" S2 F3S B1502 " pdb="FE3 F3S B1502 " ideal model delta sigma weight residual 2.300 3.932 -1.632 2.00e-02 2.50e+03 6.66e+03 ... (remaining 61203 not shown) Histogram of bond angle deviations from ideal: 41.19 - 59.76: 16 59.76 - 78.33: 128 78.33 - 96.90: 0 96.90 - 115.47: 39744 115.47 - 134.04: 43060 Bond angle restraints: 82948 Sorted by residual: angle pdb=" S1 F3S D1502 " pdb="FE4 F3S D1502 " pdb=" S3 F3S D1502 " ideal model delta sigma weight residual 114.75 64.93 49.82 3.00e+00 1.11e-01 2.76e+02 angle pdb=" S3 F3S B1502 " pdb="FE1 F3S B1502 " pdb=" S4 F3S B1502 " ideal model delta sigma weight residual 112.59 63.04 49.55 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S1 F3S C1502 " pdb="FE4 F3S C1502 " pdb=" S3 F3S C1502 " ideal model delta sigma weight residual 114.75 65.24 49.51 3.00e+00 1.11e-01 2.72e+02 angle pdb=" S1 F3S A1502 " pdb="FE4 F3S A1502 " pdb=" S3 F3S A1502 " ideal model delta sigma weight residual 114.75 65.26 49.49 3.00e+00 1.11e-01 2.72e+02 angle pdb=" S3 F3S C1502 " pdb="FE1 F3S C1502 " pdb=" S4 F3S C1502 " ideal model delta sigma weight residual 112.59 63.30 49.29 3.00e+00 1.11e-01 2.70e+02 ... (remaining 82943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 36244 35.54 - 71.07: 500 71.07 - 106.61: 41 106.61 - 142.14: 1 142.14 - 177.68: 2 Dihedral angle restraints: 36788 sinusoidal: 14876 harmonic: 21912 Sorted by residual: dihedral pdb=" CA ASP F 406 " pdb=" C ASP F 406 " pdb=" N LEU F 407 " pdb=" CA LEU F 407 " ideal model delta harmonic sigma weight residual -180.00 -145.05 -34.95 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA ASP F 412 " pdb=" C ASP F 412 " pdb=" N GLU F 413 " pdb=" CA GLU F 413 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" O5' FAD G 503 " pdb=" O3P FAD G 503 " pdb=" P FAD G 503 " pdb=" PA FAD G 503 " ideal model delta sinusoidal sigma weight residual -61.77 115.91 -177.68 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 36785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.680: 9236 0.680 - 1.359: 0 1.359 - 2.039: 0 2.039 - 2.719: 0 2.719 - 3.398: 4 Chirality restraints: 9240 Sorted by residual: chirality pdb=" S2 F3S B1502 " pdb="FE1 F3S B1502 " pdb="FE3 F3S B1502 " pdb="FE4 F3S B1502 " both_signs ideal model delta sigma weight residual False 10.77 7.37 3.40 2.00e-01 2.50e+01 2.89e+02 chirality pdb=" S2 F3S D1502 " pdb="FE1 F3S D1502 " pdb="FE3 F3S D1502 " pdb="FE4 F3S D1502 " both_signs ideal model delta sigma weight residual False 10.77 7.51 3.25 2.00e-01 2.50e+01 2.65e+02 chirality pdb=" S2 F3S A1502 " pdb="FE1 F3S A1502 " pdb="FE3 F3S A1502 " pdb="FE4 F3S A1502 " both_signs ideal model delta sigma weight residual False 10.77 7.62 3.15 2.00e-01 2.50e+01 2.49e+02 ... (remaining 9237 not shown) Planarity restraints: 10840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 69 " -0.016 2.00e-02 2.50e+03 1.74e-02 7.55e+00 pdb=" CG TRP G 69 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP G 69 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 69 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 69 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 69 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP G 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 69 " -0.015 2.00e-02 2.50e+03 1.31e-02 4.31e+00 pdb=" CG TRP F 69 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP F 69 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 69 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 69 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 69 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 268 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C THR F 268 " -0.035 2.00e-02 2.50e+03 pdb=" O THR F 268 " 0.013 2.00e-02 2.50e+03 pdb=" N SER F 269 " 0.012 2.00e-02 2.50e+03 ... (remaining 10837 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 71 2.31 - 2.96: 28548 2.96 - 3.60: 84850 3.60 - 4.25: 130934 4.25 - 4.90: 218927 Nonbonded interactions: 463330 Sorted by model distance: nonbonded pdb=" SG CYS C1102 " pdb=" S3 F3S C1502 " model vdw 1.660 3.760 nonbonded pdb=" SG CYS C1113 " pdb=" S1 F3S C1502 " model vdw 1.761 3.760 nonbonded pdb=" OE1 GLU H 125 " pdb="FE3 SF4 H 502 " model vdw 2.057 3.000 nonbonded pdb=" OE1 GLU G 125 " pdb="FE3 SF4 G 502 " model vdw 2.086 3.000 nonbonded pdb=" OE1 GLU E 125 " pdb="FE3 SF4 E 502 " model vdw 2.107 3.000 ... (remaining 463325 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.490 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 134.810 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.023 1.724 61208 Z= 1.697 Angle : 0.970 49.824 82948 Z= 0.413 Chirality : 0.078 3.398 9240 Planarity : 0.003 0.047 10840 Dihedral : 13.251 177.681 22804 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.41 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -3.05 (0.08), residues: 7728 helix: -1.20 (0.09), residues: 2760 sheet: -1.91 (0.15), residues: 1100 loop : -2.72 (0.09), residues: 3868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP G 69 HIS 0.004 0.001 HIS E 466 PHE 0.014 0.001 PHE G 36 TYR 0.012 0.001 TYR F 321 ARG 0.004 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 842 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8598 (mmm) cc_final: 0.8292 (tpp) REVERT: A 693 MET cc_start: 0.7737 (mmm) cc_final: 0.7452 (mmp) REVERT: A 710 LYS cc_start: 0.8899 (tppp) cc_final: 0.8605 (tttt) REVERT: A 726 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 742 MET cc_start: 0.7991 (mtm) cc_final: 0.7689 (mtt) REVERT: A 749 ILE cc_start: 0.9337 (tp) cc_final: 0.9100 (mm) REVERT: A 849 ILE cc_start: 0.9098 (pt) cc_final: 0.8605 (mt) REVERT: A 1039 LYS cc_start: 0.9285 (mmtt) cc_final: 0.9040 (mmmm) REVERT: A 1289 MET cc_start: 0.8567 (mpp) cc_final: 0.8239 (mtp) REVERT: B 40 THR cc_start: 0.8456 (p) cc_final: 0.8066 (p) REVERT: B 98 LEU cc_start: 0.8690 (mt) cc_final: 0.8430 (mt) REVERT: B 264 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7243 (tppt) REVERT: B 418 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7519 (ptmt) REVERT: B 1149 ILE cc_start: 0.9000 (mt) cc_final: 0.8707 (mm) REVERT: B 1344 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 1387 MET cc_start: 0.9233 (ttt) cc_final: 0.8812 (ttp) REVERT: B 1425 LYS cc_start: 0.8485 (tptm) cc_final: 0.8158 (ttpt) REVERT: B 1462 MET cc_start: 0.7690 (mmm) cc_final: 0.7315 (tpp) REVERT: C 244 MET cc_start: 0.8560 (tpp) cc_final: 0.8221 (tpp) REVERT: C 346 ASP cc_start: 0.7774 (p0) cc_final: 0.7266 (p0) REVERT: C 458 MET cc_start: 0.7925 (ppp) cc_final: 0.7559 (ppp) REVERT: C 881 LYS cc_start: 0.8608 (mttt) cc_final: 0.8404 (mtmm) REVERT: C 1013 VAL cc_start: 0.9168 (t) cc_final: 0.8899 (p) REVERT: C 1047 MET cc_start: 0.7728 (ttm) cc_final: 0.7404 (mtm) REVERT: C 1387 MET cc_start: 0.8572 (ttt) cc_final: 0.8273 (ttp) REVERT: C 1419 HIS cc_start: 0.6495 (t70) cc_final: 0.6228 (t-170) REVERT: C 1443 ILE cc_start: 0.9449 (mt) cc_final: 0.9216 (mt) REVERT: D 227 MET cc_start: 0.8795 (ttm) cc_final: 0.8578 (ttm) REVERT: D 381 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7970 (pp20) REVERT: D 562 MET cc_start: 0.7634 (mtm) cc_final: 0.7173 (mtm) REVERT: D 711 MET cc_start: 0.8757 (ptm) cc_final: 0.8300 (ptp) REVERT: D 823 MET cc_start: 0.8235 (mtp) cc_final: 0.7937 (ptp) REVERT: D 1167 LEU cc_start: 0.8899 (mt) cc_final: 0.8608 (mt) REVERT: D 1186 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7950 (ttm-80) REVERT: D 1387 MET cc_start: 0.8183 (ttt) cc_final: 0.7913 (ttt) REVERT: G 57 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8734 (tm-30) REVERT: G 69 TRP cc_start: 0.5764 (p90) cc_final: 0.5341 (p-90) REVERT: G 146 GLU cc_start: 0.8395 (pt0) cc_final: 0.7582 (tm-30) REVERT: G 223 ARG cc_start: 0.6571 (mtt180) cc_final: 0.6334 (mpt180) REVERT: G 247 ARG cc_start: 0.5537 (mtp180) cc_final: 0.5019 (mtm180) REVERT: G 328 MET cc_start: 0.5802 (tmm) cc_final: 0.5461 (tmm) REVERT: G 466 HIS cc_start: 0.8898 (t70) cc_final: 0.8637 (t70) REVERT: E 33 TYR cc_start: 0.8609 (m-80) cc_final: 0.8266 (m-80) REVERT: E 166 GLU cc_start: 0.8722 (tp30) cc_final: 0.8460 (mt-10) REVERT: E 194 PHE cc_start: 0.7491 (t80) cc_final: 0.7257 (t80) REVERT: E 328 MET cc_start: 0.8551 (ttm) cc_final: 0.8230 (ttt) REVERT: E 378 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6994 (ptm160) REVERT: E 425 LEU cc_start: 0.8201 (tp) cc_final: 0.7837 (tp) REVERT: F 463 GLU cc_start: 0.8577 (tt0) cc_final: 0.8211 (tm-30) REVERT: H 101 GLN cc_start: 0.7526 (pt0) cc_final: 0.7185 (pt0) REVERT: H 137 TRP cc_start: 0.6508 (m-10) cc_final: 0.5819 (m-10) outliers start: 0 outliers final: 0 residues processed: 842 average time/residue: 0.6678 time to fit residues: 894.2662 Evaluate side-chains 514 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 651 optimal weight: 10.0000 chunk 585 optimal weight: 30.0000 chunk 324 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 394 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 605 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 367 optimal weight: 3.9990 chunk 450 optimal weight: 4.9990 chunk 701 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 52 GLN A 223 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 240 ASN A 318 GLN A 466 HIS A 762 HIS A 872 ASN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 GLN A1107 GLN A1120 GLN A1205 ASN A1263 HIS ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN A1431 HIS B 52 GLN B 409 HIS B 422 ASN B 643 ASN B 653 HIS B 755 GLN B 824 GLN B 934 GLN B 982 GLN B1053 HIS B1205 ASN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1363 ASN B1419 HIS C 52 GLN C 109 GLN C 135 ASN C 163 GLN C 208 HIS C 214 ASN C 223 GLN C 240 ASN C 505 GLN ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS C 755 GLN C 934 GLN C 989 GLN C1169 HIS C1274 GLN ** C1282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1293 ASN C1363 ASN D 30 HIS D 52 GLN D 223 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 318 GLN D 451 GLN D 466 HIS D 603 HIS D 643 ASN D 653 HIS D 738 HIS D 755 GLN D 796 HIS D 818 ASN D 824 GLN D 934 GLN D 943 GLN D1137 ASN D1159 ASN D1184 ASN D1205 ASN D1234 ASN D1363 ASN D1419 HIS D1423 GLN D1431 HIS G 44 GLN G 258 ASN E 27 GLN E 113 GLN E 234 HIS E 270 ASN E 283 ASN F 57 GLN F 65 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN F 348 GLN H 11 HIS H 50 GLN H 175 HIS Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 61208 Z= 0.371 Angle : 0.911 75.585 82948 Z= 0.381 Chirality : 0.046 0.804 9240 Planarity : 0.004 0.060 10840 Dihedral : 6.670 176.878 8680 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.25 % Favored : 93.74 % Rotamer: Outliers : 1.56 % Allowed : 13.26 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -2.23 (0.09), residues: 7728 helix: -0.31 (0.10), residues: 2740 sheet: -1.53 (0.15), residues: 1116 loop : -2.37 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 69 HIS 0.006 0.001 HIS B 971 PHE 0.020 0.002 PHE A1254 TYR 0.015 0.001 TYR D 813 ARG 0.009 0.000 ARG G 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 521 time to evaluate : 5.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8741 (mmm) cc_final: 0.8384 (tpp) REVERT: A 726 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 742 MET cc_start: 0.7922 (mtm) cc_final: 0.7637 (mtt) REVERT: A 745 ARG cc_start: 0.8276 (mtp180) cc_final: 0.8029 (mtm180) REVERT: A 849 ILE cc_start: 0.9098 (pt) cc_final: 0.8662 (mt) REVERT: A 1039 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9104 (mmmm) REVERT: A 1249 MET cc_start: 0.8998 (mmm) cc_final: 0.8634 (mtt) REVERT: A 1289 MET cc_start: 0.8629 (mpp) cc_final: 0.8346 (mmm) REVERT: B 40 THR cc_start: 0.8563 (p) cc_final: 0.8170 (p) REVERT: B 335 MET cc_start: 0.7696 (ptp) cc_final: 0.7492 (ptp) REVERT: B 418 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7544 (ptmt) REVERT: B 811 LYS cc_start: 0.8574 (tppt) cc_final: 0.7923 (tptt) REVERT: B 860 MET cc_start: 0.7516 (ttt) cc_final: 0.7089 (ttt) REVERT: B 1182 ASP cc_start: 0.8294 (t0) cc_final: 0.7872 (t0) REVERT: B 1387 MET cc_start: 0.9251 (ttt) cc_final: 0.8818 (ttp) REVERT: B 1425 LYS cc_start: 0.8406 (tptm) cc_final: 0.8140 (ttpt) REVERT: B 1462 MET cc_start: 0.7771 (mmm) cc_final: 0.7348 (tpp) REVERT: C 244 MET cc_start: 0.8543 (tpp) cc_final: 0.8262 (tpp) REVERT: C 346 ASP cc_start: 0.7834 (p0) cc_final: 0.7307 (p0) REVERT: C 458 MET cc_start: 0.7876 (ppp) cc_final: 0.7315 (ppp) REVERT: C 881 LYS cc_start: 0.8642 (mttt) cc_final: 0.8426 (mtmm) REVERT: C 952 MET cc_start: 0.7603 (tmm) cc_final: 0.7355 (tmm) REVERT: C 1013 VAL cc_start: 0.9140 (t) cc_final: 0.8932 (p) REVERT: C 1047 MET cc_start: 0.7871 (ttm) cc_final: 0.7564 (mtm) REVERT: C 1387 MET cc_start: 0.8592 (ttt) cc_final: 0.8267 (ttp) REVERT: C 1443 ILE cc_start: 0.9409 (mt) cc_final: 0.9173 (mt) REVERT: D 227 MET cc_start: 0.8828 (ttm) cc_final: 0.8618 (ttm) REVERT: D 381 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7864 (pp20) REVERT: D 562 MET cc_start: 0.7312 (mtm) cc_final: 0.6741 (mtp) REVERT: D 711 MET cc_start: 0.8793 (ptm) cc_final: 0.8334 (ptp) REVERT: D 823 MET cc_start: 0.8150 (mtp) cc_final: 0.7856 (ptp) REVERT: D 1186 ARG cc_start: 0.8311 (mtp85) cc_final: 0.8020 (mtp85) REVERT: G 44 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: G 57 GLN cc_start: 0.9413 (tm-30) cc_final: 0.8847 (tm-30) REVERT: G 130 ASP cc_start: 0.7756 (p0) cc_final: 0.7420 (p0) REVERT: G 146 GLU cc_start: 0.8443 (pt0) cc_final: 0.7646 (tm-30) REVERT: G 183 MET cc_start: 0.6858 (ptp) cc_final: 0.6587 (ptp) REVERT: G 247 ARG cc_start: 0.5219 (mtp180) cc_final: 0.4742 (mtm180) REVERT: E 166 GLU cc_start: 0.8762 (tp30) cc_final: 0.8492 (mt-10) REVERT: E 378 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7021 (ptm160) REVERT: E 425 LEU cc_start: 0.8237 (tp) cc_final: 0.7852 (tp) REVERT: F 16 MET cc_start: 0.8189 (mmm) cc_final: 0.7987 (mmm) REVERT: F 133 TRP cc_start: 0.7865 (t60) cc_final: 0.7447 (t60) REVERT: F 463 GLU cc_start: 0.8663 (tt0) cc_final: 0.8208 (tm-30) REVERT: H 101 GLN cc_start: 0.7498 (pt0) cc_final: 0.7081 (pt0) REVERT: H 137 TRP cc_start: 0.6634 (m-10) cc_final: 0.6157 (m-10) REVERT: H 219 PHE cc_start: 0.7062 (m-80) cc_final: 0.6789 (m-10) outliers start: 98 outliers final: 66 residues processed: 584 average time/residue: 0.5784 time to fit residues: 568.9150 Evaluate side-chains 541 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 474 time to evaluate : 5.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 311 ARG Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 389 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 583 optimal weight: 5.9990 chunk 477 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 702 optimal weight: 3.9990 chunk 758 optimal weight: 6.9990 chunk 625 optimal weight: 10.0000 chunk 696 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 563 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 ASN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 61208 Z= 0.280 Angle : 0.833 70.088 82948 Z= 0.345 Chirality : 0.048 1.593 9240 Planarity : 0.004 0.054 10840 Dihedral : 6.543 172.448 8680 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 2.07 % Allowed : 15.85 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.71 (0.09), residues: 7728 helix: 0.13 (0.10), residues: 2732 sheet: -1.27 (0.15), residues: 1124 loop : -2.05 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 69 HIS 0.008 0.001 HIS H 292 PHE 0.016 0.001 PHE C1139 TYR 0.011 0.001 TYR C 696 ARG 0.005 0.000 ARG B 895 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 520 time to evaluate : 5.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8732 (mmm) cc_final: 0.8349 (tpp) REVERT: A 461 MET cc_start: 0.7928 (tmm) cc_final: 0.7528 (tmm) REVERT: A 693 MET cc_start: 0.7882 (mmp) cc_final: 0.6559 (tpt) REVERT: A 726 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 745 ARG cc_start: 0.8542 (mtp180) cc_final: 0.8134 (mtm180) REVERT: A 849 ILE cc_start: 0.9001 (pt) cc_final: 0.8617 (mt) REVERT: A 1039 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9102 (mmmm) REVERT: A 1249 MET cc_start: 0.9020 (mmm) cc_final: 0.8617 (mtm) REVERT: A 1289 MET cc_start: 0.8571 (mpp) cc_final: 0.8351 (mmm) REVERT: B 40 THR cc_start: 0.8596 (p) cc_final: 0.8189 (p) REVERT: B 360 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7296 (t0) REVERT: B 418 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7527 (ptmt) REVERT: B 811 LYS cc_start: 0.8578 (tppt) cc_final: 0.8247 (tmtt) REVERT: B 860 MET cc_start: 0.7707 (ttt) cc_final: 0.7307 (ttt) REVERT: B 1182 ASP cc_start: 0.8252 (t0) cc_final: 0.7817 (t0) REVERT: B 1344 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 1387 MET cc_start: 0.9230 (ttt) cc_final: 0.8906 (ttt) REVERT: B 1425 LYS cc_start: 0.8511 (tptm) cc_final: 0.8216 (ttpt) REVERT: B 1462 MET cc_start: 0.7755 (mmm) cc_final: 0.7307 (tpp) REVERT: C 244 MET cc_start: 0.8570 (tpp) cc_final: 0.8285 (tpp) REVERT: C 346 ASP cc_start: 0.7777 (p0) cc_final: 0.7334 (p0) REVERT: C 458 MET cc_start: 0.7904 (ppp) cc_final: 0.7382 (ppp) REVERT: C 702 ASP cc_start: 0.8053 (t0) cc_final: 0.7812 (t0) REVERT: C 881 LYS cc_start: 0.8667 (mttt) cc_final: 0.8398 (mtmm) REVERT: C 1047 MET cc_start: 0.7891 (ttm) cc_final: 0.7611 (mtm) REVERT: C 1387 MET cc_start: 0.8574 (ttt) cc_final: 0.8245 (ttp) REVERT: C 1443 ILE cc_start: 0.9397 (mt) cc_final: 0.9155 (mt) REVERT: D 381 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7858 (pp20) REVERT: D 711 MET cc_start: 0.8767 (ptm) cc_final: 0.8306 (ptp) REVERT: D 823 MET cc_start: 0.8141 (mtp) cc_final: 0.7852 (ptp) REVERT: D 1186 ARG cc_start: 0.8261 (mtp85) cc_final: 0.8028 (mtp85) REVERT: G 16 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6231 (mtp) REVERT: G 57 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8825 (tm-30) REVERT: G 130 ASP cc_start: 0.7742 (p0) cc_final: 0.7459 (p0) REVERT: G 146 GLU cc_start: 0.8623 (pt0) cc_final: 0.7738 (tm-30) REVERT: G 195 LYS cc_start: 0.6384 (mmtt) cc_final: 0.6046 (mmtm) REVERT: G 247 ARG cc_start: 0.5119 (mtp180) cc_final: 0.4629 (mtm180) REVERT: G 328 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6196 (tmm) REVERT: G 466 HIS cc_start: 0.8928 (t70) cc_final: 0.8682 (t70) REVERT: E 166 GLU cc_start: 0.8768 (tp30) cc_final: 0.8514 (mt-10) REVERT: E 378 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7029 (ptm160) REVERT: E 425 LEU cc_start: 0.8285 (tp) cc_final: 0.7913 (tp) REVERT: F 16 MET cc_start: 0.8210 (mmm) cc_final: 0.7948 (mmm) REVERT: F 133 TRP cc_start: 0.7997 (t60) cc_final: 0.7537 (t60) REVERT: F 463 GLU cc_start: 0.8645 (tt0) cc_final: 0.8263 (tm-30) REVERT: H 101 GLN cc_start: 0.7422 (pt0) cc_final: 0.6758 (pt0) REVERT: H 137 TRP cc_start: 0.6730 (m-10) cc_final: 0.6451 (m-10) REVERT: H 219 PHE cc_start: 0.7031 (m-80) cc_final: 0.6761 (m-10) outliers start: 130 outliers final: 89 residues processed: 612 average time/residue: 0.5513 time to fit residues: 575.6048 Evaluate side-chains 574 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 482 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 693 optimal weight: 10.0000 chunk 528 optimal weight: 20.0000 chunk 364 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 471 optimal weight: 5.9990 chunk 704 optimal weight: 1.9990 chunk 746 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 chunk 668 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 502 ASN A 653 HIS ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS D 695 ASN D 989 GLN D1184 ASN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 61208 Z= 0.349 Angle : 0.819 89.937 82948 Z= 0.356 Chirality : 0.052 1.840 9240 Planarity : 0.004 0.056 10840 Dihedral : 6.625 173.368 8680 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 3.12 % Allowed : 16.99 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.54 (0.09), residues: 7728 helix: 0.28 (0.10), residues: 2708 sheet: -1.16 (0.16), residues: 1124 loop : -1.96 (0.10), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 69 HIS 0.005 0.001 HIS C 796 PHE 0.026 0.002 PHE G 36 TYR 0.013 0.002 TYR B 669 ARG 0.008 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 490 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8779 (mmm) cc_final: 0.8425 (tpp) REVERT: A 693 MET cc_start: 0.7992 (mmp) cc_final: 0.6770 (tpt) REVERT: A 745 ARG cc_start: 0.8622 (mtp180) cc_final: 0.8361 (mtm180) REVERT: A 849 ILE cc_start: 0.9048 (pt) cc_final: 0.8709 (mt) REVERT: A 1039 LYS cc_start: 0.9421 (mmtt) cc_final: 0.9172 (mmmm) REVERT: A 1104 MET cc_start: 0.8636 (mmm) cc_final: 0.8310 (mmm) REVERT: A 1145 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 1246 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8360 (tt) REVERT: A 1249 MET cc_start: 0.9061 (mmm) cc_final: 0.8641 (mtm) REVERT: A 1289 MET cc_start: 0.8577 (mpp) cc_final: 0.8344 (mmm) REVERT: B 40 THR cc_start: 0.8720 (p) cc_final: 0.8309 (p) REVERT: B 360 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7225 (t0) REVERT: B 418 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7543 (ptmt) REVERT: B 860 MET cc_start: 0.7685 (ttt) cc_final: 0.7236 (ttt) REVERT: B 1182 ASP cc_start: 0.8275 (t0) cc_final: 0.7854 (t0) REVERT: B 1387 MET cc_start: 0.9266 (ttt) cc_final: 0.8993 (ttt) REVERT: B 1425 LYS cc_start: 0.8675 (tptm) cc_final: 0.8374 (ttpt) REVERT: B 1462 MET cc_start: 0.7826 (mmm) cc_final: 0.7388 (tpp) REVERT: C 458 MET cc_start: 0.8340 (ppp) cc_final: 0.7678 (ppp) REVERT: C 1047 MET cc_start: 0.7894 (ttm) cc_final: 0.7625 (mtm) REVERT: C 1173 ARG cc_start: 0.6316 (mmt180) cc_final: 0.6103 (mmt-90) REVERT: C 1387 MET cc_start: 0.8627 (ttt) cc_final: 0.8281 (ttp) REVERT: C 1443 ILE cc_start: 0.9411 (mt) cc_final: 0.9184 (mt) REVERT: D 381 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7837 (pp20) REVERT: D 491 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8751 (mttp) REVERT: D 702 ASP cc_start: 0.8630 (t0) cc_final: 0.7894 (m-30) REVERT: D 711 MET cc_start: 0.8737 (ptm) cc_final: 0.8277 (ptp) REVERT: D 823 MET cc_start: 0.8186 (mtp) cc_final: 0.7886 (ptp) REVERT: G 16 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6187 (mtp) REVERT: G 57 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8847 (tm-30) REVERT: G 130 ASP cc_start: 0.7758 (p0) cc_final: 0.7421 (p0) REVERT: G 146 GLU cc_start: 0.8540 (pt0) cc_final: 0.7653 (tm-30) REVERT: G 195 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5760 (mmtm) REVERT: G 328 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5365 (tmm) REVERT: E 166 GLU cc_start: 0.8771 (tp30) cc_final: 0.8521 (mt-10) REVERT: E 378 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7029 (ptm160) REVERT: E 425 LEU cc_start: 0.8262 (tp) cc_final: 0.7857 (tp) REVERT: F 16 MET cc_start: 0.8153 (mmm) cc_final: 0.7907 (mmm) REVERT: F 133 TRP cc_start: 0.8060 (t60) cc_final: 0.7508 (t60) REVERT: F 463 GLU cc_start: 0.8653 (tt0) cc_final: 0.8205 (tm-30) REVERT: H 101 GLN cc_start: 0.7509 (pt0) cc_final: 0.6657 (pt0) REVERT: H 137 TRP cc_start: 0.6765 (m-10) cc_final: 0.6394 (m-10) outliers start: 196 outliers final: 135 residues processed: 640 average time/residue: 0.5491 time to fit residues: 607.0172 Evaluate side-chains 611 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 471 time to evaluate : 5.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 621 optimal weight: 6.9990 chunk 423 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 555 optimal weight: 9.9990 chunk 307 optimal weight: 0.9980 chunk 636 optimal weight: 0.9990 chunk 515 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 381 optimal weight: 0.0010 chunk 669 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 HIS ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 61208 Z= 0.229 Angle : 0.769 82.978 82948 Z= 0.326 Chirality : 0.050 1.531 9240 Planarity : 0.003 0.053 10840 Dihedral : 6.407 175.998 8680 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 2.93 % Allowed : 18.36 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.29 (0.10), residues: 7728 helix: 0.47 (0.10), residues: 2720 sheet: -1.04 (0.16), residues: 1144 loop : -1.80 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 69 HIS 0.005 0.001 HIS H 292 PHE 0.020 0.001 PHE G 36 TYR 0.012 0.001 TYR H 82 ARG 0.006 0.000 ARG C 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 519 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8738 (mmm) cc_final: 0.8362 (tpp) REVERT: A 461 MET cc_start: 0.7951 (tmm) cc_final: 0.7549 (tmm) REVERT: A 693 MET cc_start: 0.7900 (mmp) cc_final: 0.6998 (tpt) REVERT: A 745 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8274 (mtm180) REVERT: A 787 ARG cc_start: 0.6647 (mmm-85) cc_final: 0.6199 (mtm180) REVERT: A 849 ILE cc_start: 0.9001 (pt) cc_final: 0.8605 (mt) REVERT: A 1039 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9154 (mmmm) REVERT: A 1104 MET cc_start: 0.8587 (mmm) cc_final: 0.8259 (mmm) REVERT: A 1145 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 1246 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 1289 MET cc_start: 0.8570 (mpp) cc_final: 0.8171 (mmm) REVERT: B 40 THR cc_start: 0.8684 (p) cc_final: 0.8265 (p) REVERT: B 360 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7210 (t0) REVERT: B 418 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7541 (ptmt) REVERT: B 743 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 811 LYS cc_start: 0.8562 (tppt) cc_final: 0.8219 (tmtt) REVERT: B 860 MET cc_start: 0.7813 (ttt) cc_final: 0.7534 (ttt) REVERT: B 1182 ASP cc_start: 0.8228 (t0) cc_final: 0.7791 (t0) REVERT: B 1344 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 1387 MET cc_start: 0.9197 (ttt) cc_final: 0.8939 (ttt) REVERT: B 1425 LYS cc_start: 0.8644 (tptm) cc_final: 0.8319 (ttpt) REVERT: B 1462 MET cc_start: 0.7813 (mmm) cc_final: 0.7305 (tpp) REVERT: C 278 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7596 (t0) REVERT: C 458 MET cc_start: 0.8315 (ppp) cc_final: 0.7506 (ppp) REVERT: C 462 GLU cc_start: 0.7481 (pp20) cc_final: 0.7278 (pp20) REVERT: C 702 ASP cc_start: 0.7784 (t0) cc_final: 0.7462 (t0) REVERT: C 1047 MET cc_start: 0.7913 (ttm) cc_final: 0.7687 (mtm) REVERT: C 1368 MET cc_start: 0.8085 (ttt) cc_final: 0.7845 (tpp) REVERT: C 1387 MET cc_start: 0.8594 (ttt) cc_final: 0.8212 (ttp) REVERT: D 345 MET cc_start: 0.8852 (mmm) cc_final: 0.8651 (mmm) REVERT: D 381 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7787 (pp20) REVERT: D 702 ASP cc_start: 0.8602 (t0) cc_final: 0.7885 (m-30) REVERT: D 711 MET cc_start: 0.8646 (ptm) cc_final: 0.8393 (ptp) REVERT: D 823 MET cc_start: 0.8175 (mtp) cc_final: 0.7860 (ptp) REVERT: G 16 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6283 (mtp) REVERT: G 57 GLN cc_start: 0.9365 (tm-30) cc_final: 0.8865 (tm-30) REVERT: G 130 ASP cc_start: 0.7734 (p0) cc_final: 0.7408 (p0) REVERT: G 146 GLU cc_start: 0.8558 (pt0) cc_final: 0.7650 (tm-30) REVERT: G 195 LYS cc_start: 0.6203 (mmtt) cc_final: 0.5877 (mmtm) REVERT: G 328 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5459 (tmm) REVERT: E 33 TYR cc_start: 0.8627 (m-80) cc_final: 0.8298 (m-80) REVERT: E 166 GLU cc_start: 0.8758 (tp30) cc_final: 0.8540 (mt-10) REVERT: E 378 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7105 (ptm160) REVERT: E 425 LEU cc_start: 0.8221 (tp) cc_final: 0.7847 (tp) REVERT: E 432 MET cc_start: 0.7877 (ttt) cc_final: 0.7522 (ttt) REVERT: F 16 MET cc_start: 0.8231 (mmm) cc_final: 0.8016 (mmm) REVERT: F 133 TRP cc_start: 0.8070 (t60) cc_final: 0.7515 (t60) REVERT: F 463 GLU cc_start: 0.8638 (tt0) cc_final: 0.8264 (tm-30) REVERT: H 101 GLN cc_start: 0.7532 (pt0) cc_final: 0.6663 (pt0) REVERT: H 137 TRP cc_start: 0.7215 (m-10) cc_final: 0.6636 (m-10) REVERT: H 436 ASP cc_start: 0.8478 (t0) cc_final: 0.8273 (t0) outliers start: 184 outliers final: 128 residues processed: 655 average time/residue: 0.5514 time to fit residues: 620.7954 Evaluate side-chains 613 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 479 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1256 MET Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1288 VAL Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 421 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 251 optimal weight: 1.9990 chunk 672 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 438 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 746 optimal weight: 20.0000 chunk 620 optimal weight: 0.9990 chunk 345 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN D 695 ASN D1184 ASN G 312 GLN E 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 61208 Z= 0.325 Angle : 0.807 83.859 82948 Z= 0.350 Chirality : 0.052 1.551 9240 Planarity : 0.004 0.054 10840 Dihedral : 6.467 177.764 8680 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.72 % Favored : 93.27 % Rotamer: Outliers : 3.46 % Allowed : 19.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.25 (0.10), residues: 7728 helix: 0.52 (0.10), residues: 2696 sheet: -0.89 (0.16), residues: 1092 loop : -1.81 (0.10), residues: 3940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 69 HIS 0.005 0.001 HIS D 868 PHE 0.020 0.001 PHE G 36 TYR 0.013 0.001 TYR G 82 ARG 0.009 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 488 time to evaluate : 5.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8749 (mmm) cc_final: 0.8418 (tpp) REVERT: A 787 ARG cc_start: 0.6693 (mmm-85) cc_final: 0.6198 (mtm180) REVERT: A 849 ILE cc_start: 0.8916 (pt) cc_final: 0.8678 (mt) REVERT: A 1039 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9179 (mmmm) REVERT: A 1145 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 1246 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 1289 MET cc_start: 0.8580 (mpp) cc_final: 0.8193 (mmm) REVERT: B 40 THR cc_start: 0.8773 (p) cc_final: 0.8382 (p) REVERT: B 360 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7225 (t0) REVERT: B 418 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7514 (ptmt) REVERT: B 844 GLU cc_start: 0.8473 (pm20) cc_final: 0.8249 (pm20) REVERT: B 860 MET cc_start: 0.7884 (ttt) cc_final: 0.7588 (ttt) REVERT: B 1182 ASP cc_start: 0.8315 (t0) cc_final: 0.7878 (t0) REVERT: B 1387 MET cc_start: 0.9249 (ttt) cc_final: 0.9000 (ttt) REVERT: B 1462 MET cc_start: 0.7872 (mmm) cc_final: 0.7351 (tpp) REVERT: C 233 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 390 MET cc_start: 0.7978 (ptp) cc_final: 0.7734 (ptm) REVERT: C 458 MET cc_start: 0.8290 (ppp) cc_final: 0.7658 (ppp) REVERT: C 702 ASP cc_start: 0.7909 (t0) cc_final: 0.7540 (t0) REVERT: C 1047 MET cc_start: 0.7897 (ttm) cc_final: 0.7683 (mtm) REVERT: C 1368 MET cc_start: 0.8180 (ttt) cc_final: 0.7930 (tpp) REVERT: C 1387 MET cc_start: 0.8622 (ttt) cc_final: 0.8224 (ttp) REVERT: D 381 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7817 (pp20) REVERT: D 491 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8480 (mmtp) REVERT: D 702 ASP cc_start: 0.8613 (t0) cc_final: 0.7902 (m-30) REVERT: D 711 MET cc_start: 0.8765 (ptm) cc_final: 0.8413 (ptp) REVERT: D 823 MET cc_start: 0.8223 (mtp) cc_final: 0.7909 (ptp) REVERT: D 1084 MET cc_start: 0.8671 (mmt) cc_final: 0.8392 (mmp) REVERT: G 16 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6299 (mtp) REVERT: G 57 GLN cc_start: 0.9374 (tm-30) cc_final: 0.8871 (tm-30) REVERT: G 130 ASP cc_start: 0.7777 (p0) cc_final: 0.7420 (p0) REVERT: G 195 LYS cc_start: 0.6214 (mmtt) cc_final: 0.5858 (mmtm) REVERT: G 328 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5432 (tmm) REVERT: E 166 GLU cc_start: 0.8767 (tp30) cc_final: 0.8545 (mt-10) REVERT: E 378 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7093 (ptm160) REVERT: E 425 LEU cc_start: 0.8253 (tp) cc_final: 0.7875 (tp) REVERT: E 432 MET cc_start: 0.7928 (ttt) cc_final: 0.7575 (ttt) REVERT: F 133 TRP cc_start: 0.8160 (t60) cc_final: 0.7630 (t60) REVERT: F 450 LEU cc_start: 0.8906 (mm) cc_final: 0.8699 (mt) REVERT: F 463 GLU cc_start: 0.8652 (tt0) cc_final: 0.8198 (tm-30) REVERT: H 101 GLN cc_start: 0.7564 (pt0) cc_final: 0.6698 (pt0) REVERT: H 137 TRP cc_start: 0.7234 (m-10) cc_final: 0.6604 (m-10) outliers start: 217 outliers final: 173 residues processed: 658 average time/residue: 0.5424 time to fit residues: 620.0275 Evaluate side-chains 648 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 470 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1294 ASP Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 421 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 720 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 545 optimal weight: 2.9990 chunk 422 optimal weight: 5.9990 chunk 628 optimal weight: 9.9990 chunk 417 optimal weight: 9.9990 chunk 744 optimal weight: 8.9990 chunk 465 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 497 HIS ** C 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 HIS D1120 GLN G 44 GLN ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN F 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 61208 Z= 0.336 Angle : 0.817 83.803 82948 Z= 0.356 Chirality : 0.052 1.545 9240 Planarity : 0.004 0.052 10840 Dihedral : 6.488 179.800 8680 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.29 % Favored : 93.70 % Rotamer: Outliers : 3.79 % Allowed : 19.90 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.22 (0.10), residues: 7728 helix: 0.51 (0.10), residues: 2692 sheet: -0.92 (0.16), residues: 1092 loop : -1.75 (0.10), residues: 3944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 69 HIS 0.008 0.001 HIS C 603 PHE 0.021 0.002 PHE G 36 TYR 0.012 0.002 TYR G 82 ARG 0.008 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 476 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.9176 (tpp) cc_final: 0.8814 (tpt) REVERT: A 293 MET cc_start: 0.8759 (mmm) cc_final: 0.8464 (tpp) REVERT: A 461 MET cc_start: 0.8054 (tmm) cc_final: 0.7673 (tmm) REVERT: A 693 MET cc_start: 0.7751 (mmp) cc_final: 0.7235 (mmm) REVERT: A 787 ARG cc_start: 0.6705 (mmm-85) cc_final: 0.6204 (mtm180) REVERT: A 849 ILE cc_start: 0.8934 (pt) cc_final: 0.8720 (mt) REVERT: A 1039 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9166 (mmmm) REVERT: A 1142 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (mm) REVERT: A 1145 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 1246 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 1289 MET cc_start: 0.8629 (mpp) cc_final: 0.8218 (mmm) REVERT: B 40 THR cc_start: 0.8811 (p) cc_final: 0.8431 (p) REVERT: B 335 MET cc_start: 0.7871 (ptp) cc_final: 0.7427 (ptp) REVERT: B 360 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7110 (t0) REVERT: B 418 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7509 (ptmt) REVERT: B 844 GLU cc_start: 0.8537 (pm20) cc_final: 0.8294 (pm20) REVERT: B 860 MET cc_start: 0.7960 (ttt) cc_final: 0.7745 (ttt) REVERT: B 1182 ASP cc_start: 0.8313 (t0) cc_final: 0.7872 (t0) REVERT: B 1387 MET cc_start: 0.9295 (ttt) cc_final: 0.9071 (ttt) REVERT: B 1462 MET cc_start: 0.7949 (mmm) cc_final: 0.7385 (tpp) REVERT: C 390 MET cc_start: 0.8039 (ptp) cc_final: 0.7770 (ptm) REVERT: C 458 MET cc_start: 0.8291 (ppp) cc_final: 0.7576 (ppp) REVERT: C 702 ASP cc_start: 0.7978 (t0) cc_final: 0.7624 (t0) REVERT: C 1368 MET cc_start: 0.8239 (ttt) cc_final: 0.7983 (tpp) REVERT: C 1387 MET cc_start: 0.8635 (ttt) cc_final: 0.8242 (ttp) REVERT: D 381 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7826 (pp20) REVERT: D 479 MET cc_start: 0.8900 (tpp) cc_final: 0.8365 (tpt) REVERT: D 702 ASP cc_start: 0.8572 (t0) cc_final: 0.7837 (m-30) REVERT: D 711 MET cc_start: 0.8752 (ptm) cc_final: 0.8487 (ptp) REVERT: D 823 MET cc_start: 0.8234 (mtp) cc_final: 0.7927 (ptp) REVERT: D 1084 MET cc_start: 0.8654 (mmt) cc_final: 0.8338 (mmt) REVERT: G 16 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6363 (mtp) REVERT: G 44 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7539 (mm-40) REVERT: G 57 GLN cc_start: 0.9370 (tm-30) cc_final: 0.8894 (tm-30) REVERT: G 130 ASP cc_start: 0.7748 (p0) cc_final: 0.7391 (p0) REVERT: G 186 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7044 (pp) REVERT: G 195 LYS cc_start: 0.6205 (mmtt) cc_final: 0.5841 (mmtm) REVERT: G 328 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5412 (tmm) REVERT: E 378 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7110 (ptm160) REVERT: E 425 LEU cc_start: 0.8270 (tp) cc_final: 0.7899 (tp) REVERT: E 432 MET cc_start: 0.7888 (ttt) cc_final: 0.7547 (ttt) REVERT: F 6 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: F 133 TRP cc_start: 0.8203 (t60) cc_final: 0.7673 (t60) REVERT: F 463 GLU cc_start: 0.8657 (tt0) cc_final: 0.8203 (tm-30) REVERT: H 101 GLN cc_start: 0.7567 (pt0) cc_final: 0.6714 (pt0) REVERT: H 286 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6056 (pp) outliers start: 238 outliers final: 187 residues processed: 664 average time/residue: 0.5787 time to fit residues: 667.0931 Evaluate side-chains 660 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 464 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1294 ASP Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 421 TRP Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 460 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 444 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 473 optimal weight: 10.0000 chunk 506 optimal weight: 4.9990 chunk 367 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 584 optimal weight: 0.3980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN ** D 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 61208 Z= 0.204 Angle : 0.771 83.538 82948 Z= 0.326 Chirality : 0.050 1.530 9240 Planarity : 0.003 0.051 10840 Dihedral : 6.257 178.618 8680 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.96 % Favored : 95.03 % Rotamer: Outliers : 3.25 % Allowed : 20.65 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.00 (0.10), residues: 7728 helix: 0.69 (0.10), residues: 2696 sheet: -0.84 (0.16), residues: 1132 loop : -1.61 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 69 HIS 0.006 0.001 HIS H 292 PHE 0.016 0.001 PHE G 36 TYR 0.013 0.001 TYR G 82 ARG 0.008 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 505 time to evaluate : 5.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8733 (mmm) cc_final: 0.8393 (tpp) REVERT: A 461 MET cc_start: 0.7987 (tmm) cc_final: 0.7604 (tmm) REVERT: A 693 MET cc_start: 0.7747 (mmp) cc_final: 0.7269 (mmm) REVERT: A 787 ARG cc_start: 0.6707 (mmm-85) cc_final: 0.6236 (mtm180) REVERT: A 849 ILE cc_start: 0.9022 (pt) cc_final: 0.8653 (mt) REVERT: A 1039 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9145 (mmmm) REVERT: A 1142 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 1145 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 1246 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 1289 MET cc_start: 0.8556 (mpp) cc_final: 0.8183 (mmm) REVERT: B 40 THR cc_start: 0.8749 (p) cc_final: 0.8352 (p) REVERT: B 335 MET cc_start: 0.7785 (ptp) cc_final: 0.7360 (ptp) REVERT: B 360 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7117 (t0) REVERT: B 418 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7568 (ptmt) REVERT: B 1051 GLU cc_start: 0.7679 (tt0) cc_final: 0.7338 (tt0) REVERT: B 1182 ASP cc_start: 0.8211 (t0) cc_final: 0.7748 (t0) REVERT: B 1387 MET cc_start: 0.9182 (ttt) cc_final: 0.8942 (ttt) REVERT: B 1462 MET cc_start: 0.7940 (mmm) cc_final: 0.7364 (tpp) REVERT: C 390 MET cc_start: 0.7942 (ptp) cc_final: 0.7696 (ptm) REVERT: C 458 MET cc_start: 0.8270 (ppp) cc_final: 0.7639 (ppp) REVERT: C 702 ASP cc_start: 0.8043 (t0) cc_final: 0.7666 (t0) REVERT: C 850 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8233 (ttm110) REVERT: C 1387 MET cc_start: 0.8546 (ttt) cc_final: 0.8246 (ttp) REVERT: D 227 MET cc_start: 0.8750 (tpt) cc_final: 0.8437 (tpp) REVERT: D 381 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7765 (pp20) REVERT: D 702 ASP cc_start: 0.8463 (t0) cc_final: 0.7743 (m-30) REVERT: D 711 MET cc_start: 0.8734 (ptm) cc_final: 0.8486 (ptp) REVERT: D 823 MET cc_start: 0.8202 (mtp) cc_final: 0.7896 (ptp) REVERT: D 1084 MET cc_start: 0.8643 (mmt) cc_final: 0.8347 (mmp) REVERT: G 16 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6155 (mtp) REVERT: G 57 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8891 (tm-30) REVERT: G 130 ASP cc_start: 0.7612 (p0) cc_final: 0.7324 (p0) REVERT: G 186 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7069 (pp) REVERT: G 195 LYS cc_start: 0.6156 (mmtt) cc_final: 0.5840 (mmtm) REVERT: G 328 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5448 (tmm) REVERT: E 33 TYR cc_start: 0.8596 (m-80) cc_final: 0.8352 (m-80) REVERT: E 378 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7191 (ptm160) REVERT: E 425 LEU cc_start: 0.8273 (tp) cc_final: 0.7900 (tp) REVERT: E 432 MET cc_start: 0.7902 (ttt) cc_final: 0.7552 (ttt) REVERT: F 133 TRP cc_start: 0.8244 (t60) cc_final: 0.7736 (t60) REVERT: F 463 GLU cc_start: 0.8593 (tt0) cc_final: 0.8208 (tm-30) REVERT: H 101 GLN cc_start: 0.7509 (pt0) cc_final: 0.6666 (pt0) REVERT: H 286 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6089 (pp) outliers start: 204 outliers final: 165 residues processed: 659 average time/residue: 0.5380 time to fit residues: 615.1177 Evaluate side-chains 649 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 476 time to evaluate : 6.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1256 MET Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1288 VAL Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1326 THR Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1452 THR Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 850 ARG Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1265 THR Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain C residue 1435 THR Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain D residue 1415 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 421 TRP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 676 optimal weight: 10.0000 chunk 712 optimal weight: 1.9990 chunk 650 optimal weight: 1.9990 chunk 693 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 626 optimal weight: 0.9990 chunk 655 optimal weight: 9.9990 chunk 690 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1320 ASN ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS F 11 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 61208 Z= 0.183 Angle : 0.763 83.427 82948 Z= 0.320 Chirality : 0.049 1.539 9240 Planarity : 0.003 0.045 10840 Dihedral : 6.069 177.374 8680 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.50 % Favored : 95.48 % Rotamer: Outliers : 2.84 % Allowed : 21.32 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.10), residues: 7728 helix: 0.84 (0.10), residues: 2696 sheet: -0.70 (0.16), residues: 1132 loop : -1.50 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 69 HIS 0.007 0.001 HIS B 603 PHE 0.019 0.001 PHE G 36 TYR 0.012 0.001 TYR H 468 ARG 0.007 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 521 time to evaluate : 5.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8737 (mmm) cc_final: 0.8382 (tpp) REVERT: A 461 MET cc_start: 0.7975 (tmm) cc_final: 0.7591 (tmm) REVERT: A 693 MET cc_start: 0.7847 (mmp) cc_final: 0.7442 (mmm) REVERT: A 787 ARG cc_start: 0.6736 (mmm-85) cc_final: 0.6304 (mtm180) REVERT: A 849 ILE cc_start: 0.8996 (pt) cc_final: 0.8605 (mt) REVERT: A 1039 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9136 (mmmm) REVERT: A 1246 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8167 (tt) REVERT: A 1289 MET cc_start: 0.8551 (mpp) cc_final: 0.8172 (mmm) REVERT: B 40 THR cc_start: 0.8698 (p) cc_final: 0.8301 (p) REVERT: B 345 MET cc_start: 0.8490 (tpp) cc_final: 0.7961 (ttp) REVERT: B 360 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7200 (t0) REVERT: B 418 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7567 (ptmt) REVERT: B 1051 GLU cc_start: 0.7668 (tt0) cc_final: 0.7341 (tt0) REVERT: B 1182 ASP cc_start: 0.8475 (t0) cc_final: 0.8016 (t0) REVERT: B 1387 MET cc_start: 0.9152 (ttt) cc_final: 0.8905 (ttt) REVERT: B 1462 MET cc_start: 0.7935 (mmm) cc_final: 0.7370 (tpp) REVERT: C 233 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 278 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7564 (t0) REVERT: C 458 MET cc_start: 0.8287 (ppp) cc_final: 0.7832 (ppp) REVERT: C 702 ASP cc_start: 0.8035 (t0) cc_final: 0.7638 (t0) REVERT: C 850 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8228 (ttm110) REVERT: C 1387 MET cc_start: 0.8523 (ttt) cc_final: 0.8299 (ttt) REVERT: D 227 MET cc_start: 0.8692 (tpt) cc_final: 0.8379 (tpp) REVERT: D 381 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7689 (pp20) REVERT: D 702 ASP cc_start: 0.8385 (t0) cc_final: 0.7621 (m-30) REVERT: D 711 MET cc_start: 0.8751 (ptm) cc_final: 0.8524 (ptp) REVERT: D 823 MET cc_start: 0.8228 (mtp) cc_final: 0.7916 (ptp) REVERT: D 1084 MET cc_start: 0.8630 (mmt) cc_final: 0.8315 (mmp) REVERT: G 16 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6103 (mtp) REVERT: G 57 GLN cc_start: 0.9351 (tm-30) cc_final: 0.8892 (tm-30) REVERT: G 68 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (p0) REVERT: G 130 ASP cc_start: 0.7800 (p0) cc_final: 0.7447 (p0) REVERT: G 195 LYS cc_start: 0.6120 (mmtt) cc_final: 0.5849 (mmtm) REVERT: G 244 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5154 (m-10) REVERT: G 328 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5490 (tmm) REVERT: E 33 TYR cc_start: 0.8588 (m-80) cc_final: 0.8340 (m-80) REVERT: E 378 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7191 (ptm160) REVERT: E 425 LEU cc_start: 0.8252 (tp) cc_final: 0.7874 (tp) REVERT: E 432 MET cc_start: 0.7873 (ttt) cc_final: 0.7552 (ttt) REVERT: F 29 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: F 133 TRP cc_start: 0.8190 (t60) cc_final: 0.7805 (t60) REVERT: F 463 GLU cc_start: 0.8588 (tt0) cc_final: 0.8130 (tm-30) REVERT: H 16 MET cc_start: 0.8077 (tpp) cc_final: 0.7874 (tpp) REVERT: H 101 GLN cc_start: 0.7478 (pt0) cc_final: 0.6664 (pt0) REVERT: H 286 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6069 (pp) outliers start: 178 outliers final: 146 residues processed: 656 average time/residue: 0.5580 time to fit residues: 636.1380 Evaluate side-chains 644 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 488 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1256 MET Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1288 VAL Chi-restraints excluded: chain B residue 1294 ASP Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1452 THR Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 850 ARG Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1265 THR Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1182 ASP Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 244 TYR Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 455 optimal weight: 4.9990 chunk 733 optimal weight: 10.0000 chunk 447 optimal weight: 8.9990 chunk 347 optimal weight: 7.9990 chunk 509 optimal weight: 1.9990 chunk 769 optimal weight: 4.9990 chunk 707 optimal weight: 6.9990 chunk 612 optimal weight: 0.1980 chunk 63 optimal weight: 9.9990 chunk 473 optimal weight: 4.9990 chunk 375 optimal weight: 0.0670 overall best weight: 2.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 HIS ** C1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1184 ASN ** D1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 61208 Z= 0.207 Angle : 0.778 83.520 82948 Z= 0.327 Chirality : 0.050 1.543 9240 Planarity : 0.003 0.053 10840 Dihedral : 6.023 176.601 8680 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.72 % Allowed : 21.69 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.77 (0.10), residues: 7728 helix: 0.86 (0.10), residues: 2692 sheet: -0.73 (0.16), residues: 1152 loop : -1.44 (0.10), residues: 3884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 69 HIS 0.005 0.001 HIS A 208 PHE 0.020 0.001 PHE F 29 TYR 0.012 0.001 TYR G 82 ARG 0.007 0.000 ARG H 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15456 Ramachandran restraints generated. 7728 Oldfield, 0 Emsley, 7728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 497 time to evaluate : 5.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8744 (mmm) cc_final: 0.8403 (tpp) REVERT: A 461 MET cc_start: 0.7964 (tmm) cc_final: 0.7742 (tmm) REVERT: A 693 MET cc_start: 0.7773 (mmp) cc_final: 0.7340 (mmm) REVERT: A 787 ARG cc_start: 0.6777 (mmm-85) cc_final: 0.6294 (mtm180) REVERT: A 849 ILE cc_start: 0.8999 (pt) cc_final: 0.8620 (mt) REVERT: A 1039 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9144 (mmmm) REVERT: A 1246 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (tt) REVERT: A 1289 MET cc_start: 0.8541 (mpp) cc_final: 0.8162 (mmm) REVERT: B 40 THR cc_start: 0.8715 (p) cc_final: 0.8320 (p) REVERT: B 335 MET cc_start: 0.7592 (ptp) cc_final: 0.7260 (ptp) REVERT: B 345 MET cc_start: 0.8518 (tpp) cc_final: 0.8018 (mtp) REVERT: B 360 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7229 (t0) REVERT: B 418 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7576 (ptmt) REVERT: B 952 MET cc_start: 0.7527 (tmm) cc_final: 0.7116 (tmt) REVERT: B 1051 GLU cc_start: 0.7678 (tt0) cc_final: 0.7354 (tt0) REVERT: B 1182 ASP cc_start: 0.8372 (t0) cc_final: 0.7967 (t0) REVERT: B 1387 MET cc_start: 0.9187 (ttt) cc_final: 0.8911 (ttt) REVERT: B 1462 MET cc_start: 0.7941 (mmm) cc_final: 0.7367 (tpp) REVERT: C 233 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 264 LYS cc_start: 0.7347 (mmmt) cc_final: 0.7096 (mmmt) REVERT: C 278 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7568 (t0) REVERT: C 458 MET cc_start: 0.8294 (ppp) cc_final: 0.7844 (ppp) REVERT: C 702 ASP cc_start: 0.8035 (t0) cc_final: 0.7644 (t0) REVERT: C 850 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8240 (ttm110) REVERT: D 227 MET cc_start: 0.8679 (tpt) cc_final: 0.8348 (tpp) REVERT: D 244 MET cc_start: 0.8928 (tpt) cc_final: 0.8610 (tpt) REVERT: D 381 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7687 (pp20) REVERT: D 702 ASP cc_start: 0.8396 (t0) cc_final: 0.7624 (m-30) REVERT: D 711 MET cc_start: 0.8771 (ptm) cc_final: 0.8543 (ptp) REVERT: D 823 MET cc_start: 0.8361 (mtp) cc_final: 0.8078 (ptp) REVERT: D 1084 MET cc_start: 0.8619 (mmt) cc_final: 0.8347 (mmp) REVERT: G 16 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6103 (mtp) REVERT: G 57 GLN cc_start: 0.9347 (tm-30) cc_final: 0.8879 (tm-30) REVERT: G 68 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8148 (p0) REVERT: G 130 ASP cc_start: 0.7796 (p0) cc_final: 0.7432 (p0) REVERT: G 328 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5494 (tmm) REVERT: E 33 TYR cc_start: 0.8592 (m-80) cc_final: 0.8364 (m-80) REVERT: E 378 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7199 (ptm160) REVERT: E 425 LEU cc_start: 0.8254 (tp) cc_final: 0.7874 (tp) REVERT: E 432 MET cc_start: 0.7877 (ttt) cc_final: 0.7565 (ttt) REVERT: F 133 TRP cc_start: 0.8249 (t60) cc_final: 0.7813 (t60) REVERT: F 463 GLU cc_start: 0.8602 (tt0) cc_final: 0.8139 (tm-30) REVERT: H 101 GLN cc_start: 0.7473 (pt0) cc_final: 0.6666 (pt0) REVERT: H 286 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6084 (pp) outliers start: 171 outliers final: 155 residues processed: 627 average time/residue: 0.5575 time to fit residues: 608.1050 Evaluate side-chains 652 residues out of total 6276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 489 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 CYS Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1256 MET Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1291 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1178 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1288 VAL Chi-restraints excluded: chain B residue 1294 ASP Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1452 THR Chi-restraints excluded: chain B residue 1468 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 724 ASN Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 850 ARG Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1265 THR Chi-restraints excluded: chain C residue 1435 THR Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 984 ILE Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 996 VAL Chi-restraints excluded: chain D residue 997 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1360 CYS Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 444 ILE Chi-restraints excluded: chain H residue 194 PHE Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 428 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 486 optimal weight: 0.3980 chunk 652 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 564 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 613 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 629 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1184 ASN G 44 GLN G 270 ASN H 332 GLN ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080701 restraints weight = 157069.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082724 restraints weight = 86064.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084078 restraints weight = 55569.427| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 61208 Z= 0.206 Angle : 0.776 83.517 82948 Z= 0.325 Chirality : 0.050 1.541 9240 Planarity : 0.003 0.055 10840 Dihedral : 5.925 175.475 8680 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.98 % Allowed : 21.56 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.72 (0.10), residues: 7728 helix: 0.91 (0.10), residues: 2692 sheet: -0.67 (0.16), residues: 1148 loop : -1.43 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 69 HIS 0.005 0.001 HIS B 603 PHE 0.017 0.001 PHE G 36 TYR 0.011 0.001 TYR G 82 ARG 0.007 0.000 ARG D1186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10690.44 seconds wall clock time: 190 minutes 30.92 seconds (11430.92 seconds total)