Starting phenix.real_space_refine on Tue Mar 19 21:16:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tga_10496/03_2024/6tga_10496_updated.pdb" } resolution = 3.26 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= 0.004 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: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 48 7.16 5 P 10 5.49 5 S 232 5.16 5 C 15776 2.51 5 N 4532 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 211": "NH1" <-> "NH2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ARG 451": "NH1" <-> "NH2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E GLU 621": "OE1" <-> "OE2" Residue "E GLU 631": "OE1" <-> "OE2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E GLU 645": "OE1" <-> "OE2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E ARG 719": "NH1" <-> "NH2" Residue "E GLU 770": "OE1" <-> "OE2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E GLU 784": "OE1" <-> "OE2" Residue "E GLU 796": "OE1" <-> "OE2" Residue "E ARG 800": "NH1" <-> "NH2" Residue "E ARG 804": "NH1" <-> "NH2" Residue "E ARG 841": "NH1" <-> "NH2" Residue "E ARG 853": "NH1" <-> "NH2" Residue "E ARG 873": "NH1" <-> "NH2" Residue "E ARG 953": "NH1" <-> "NH2" Residue "E GLU 955": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 361": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 439": "NH1" <-> "NH2" Residue "F ARG 446": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "H ARG 8": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25324 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7261 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 55, 'TRANS': 893} Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3645 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 30, 'TRANS': 462} Chain: "G" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1076 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "D" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 505 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 8, 'TRANS': 60} Chain: "E" Number of atoms: 7261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7261 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 55, 'TRANS': 893} Chain: "F" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3645 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 30, 'TRANS': 462} Chain: "C" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1076 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 505 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 8, 'TRANS': 60} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'H2S': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'H2S': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2875 SG CYS A 386 116.556 69.425 78.410 1.00 6.09 S ATOM 368 SG CYS A 57 89.219 94.275 56.606 1.00 8.15 S ATOM 442 SG CYS A 68 85.474 94.995 55.951 1.00 3.98 S ATOM 467 SG CYS A 71 84.557 97.849 59.408 1.00 5.50 S ATOM 568 SG CYS A 85 88.262 98.592 59.851 1.00 7.04 S ATOM 909 SG CYS A 130 83.391 81.453 53.387 1.00 4.61 S ATOM 852 SG CYS A 121 79.099 79.273 49.052 1.00 2.95 S ATOM 873 SG CYS A 124 84.958 75.817 49.774 1.00 3.21 S ATOM 1347 SG CYS A 185 90.941 88.646 53.416 1.00 9.80 S ATOM 1326 SG CYS A 182 92.850 86.054 47.794 1.00 4.41 S ATOM 1698 SG CYS A 234 91.780 81.968 53.123 1.00 7.16 S ATOM 1372 SG CYS A 188 97.011 86.071 52.504 1.00 3.22 S ATOM 1671 SG CYS A 230 98.808 80.330 55.534 1.00 9.80 S ATOM 1637 SG CYS A 224 104.503 78.220 54.814 1.00 3.75 S ATOM 1656 SG CYS A 227 102.601 80.080 60.920 1.00 4.59 S ATOM 1401 SG CYS A 192 103.977 84.451 56.575 1.00 9.80 S ATOM 1879 SG CYS A 258 102.858 70.500 70.464 1.00 4.29 S ATOM 2135 SG CYS A 293 105.400 74.121 66.122 1.00 1.82 S ATOM 1902 SG CYS A 261 108.358 74.594 72.028 1.00 5.49 S ATOM 1923 SG CYS A 265 102.440 76.972 71.241 1.00 4.42 S ATOM 10736 SG CYS B 471 92.016 106.310 46.912 1.00 2.23 S ATOM 10464 SG CYS B 433 90.388 101.454 42.898 1.00 1.99 S ATOM 10444 SG CYS B 430 88.688 100.837 48.933 1.00 9.80 S ATOM 10427 SG CYS B 427 95.203 100.641 47.206 1.00 4.11 S ATOM 11482 SG CYS G 77 98.517 111.382 28.371 1.00 10.11 S ATOM 11518 SG CYS G 82 98.221 114.214 26.470 1.00 10.17 S ATOM 11763 SG CYS G 116 100.079 114.499 32.379 1.00 9.16 S ATOM 11789 SG CYS G 120 98.851 117.830 30.897 1.00 11.13 S ATOM 15362 SG CYS E 386 36.669 86.314 78.414 1.00 6.01 S ATOM 12855 SG CYS E 57 64.006 61.470 56.611 1.00 8.30 S ATOM 12929 SG CYS E 68 67.755 60.750 55.954 1.00 4.20 S ATOM 12954 SG CYS E 71 68.673 57.896 59.411 1.00 5.45 S ATOM 13055 SG CYS E 85 64.968 57.153 59.854 1.00 7.48 S ATOM 13396 SG CYS E 130 69.836 74.292 53.391 1.00 3.86 S ATOM 13339 SG CYS E 121 74.128 76.474 49.056 1.00 3.03 S ATOM 13360 SG CYS E 124 68.268 79.929 49.779 1.00 2.73 S ATOM 13834 SG CYS E 185 62.288 67.098 53.420 1.00 9.80 S ATOM 13813 SG CYS E 182 60.378 69.691 47.798 1.00 3.21 S ATOM 14185 SG CYS E 234 61.447 73.776 53.127 1.00 5.48 S ATOM 13859 SG CYS E 188 56.217 69.673 52.507 1.00 3.69 S ATOM 14158 SG CYS E 230 54.419 75.413 55.538 1.00 9.80 S ATOM 14124 SG CYS E 224 48.729 77.522 54.813 1.00 4.21 S ATOM 14143 SG CYS E 227 50.642 75.663 60.926 1.00 2.20 S ATOM 13888 SG CYS E 192 49.251 71.292 56.578 1.00 9.80 S ATOM 14366 SG CYS E 258 50.367 85.241 70.468 1.00 4.42 S ATOM 14622 SG CYS E 293 47.826 81.620 66.126 1.00 9.80 S ATOM 14389 SG CYS E 261 44.868 81.147 72.032 1.00 5.25 S ATOM 14410 SG CYS E 265 50.786 78.770 71.245 1.00 4.13 S ATOM 23223 SG CYS F 471 61.219 49.436 46.915 1.00 1.95 S ATOM 22951 SG CYS F 433 62.847 54.292 42.901 1.00 1.49 S ATOM 22931 SG CYS F 430 64.546 54.909 48.936 1.00 3.24 S ATOM 22914 SG CYS F 427 58.031 55.105 47.209 1.00 4.24 S ATOM 23969 SG CYS C 77 54.720 44.363 28.374 1.00 10.14 S ATOM 24005 SG CYS C 82 55.016 41.531 26.473 1.00 9.72 S ATOM 24250 SG CYS C 116 53.157 41.246 32.382 1.00 9.28 S ATOM 24276 SG CYS C 120 54.386 37.915 30.900 1.00 10.98 S Time building chain proxies: 13.92, per 1000 atoms: 0.55 Number of scatterers: 25324 At special positions: 0 Unit cell: (153.86, 155.744, 116.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mo 2 41.97 Fe 48 26.01 S 232 16.00 P 10 15.00 O 4724 8.00 N 4532 7.00 C 15776 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 68 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 71 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 85 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 82 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 77 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 116 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 120 " pdb=" FES E1004 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 68 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 71 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 85 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 57 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 82 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 77 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 116 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 120 " pdb=" SF4 A1005 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 121 " pdb="FE4 SF4 A1005 " - pdb=" NE2 HIS A 117 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 124 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 130 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 182 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 234 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 188 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb=" SF4 A1007 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb=" SF4 B 602 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 433 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 430 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 427 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 471 " pdb=" SF4 E1005 " pdb="FE2 SF4 E1005 " - pdb=" SG CYS E 121 " pdb="FE4 SF4 E1005 " - pdb=" NE2 HIS E 117 " pdb="FE3 SF4 E1005 " - pdb=" SG CYS E 124 " pdb="FE1 SF4 E1005 " - pdb=" SG CYS E 130 " pdb=" SF4 E1006 " pdb="FE2 SF4 E1006 " - pdb=" SG CYS E 182 " pdb="FE3 SF4 E1006 " - pdb=" SG CYS E 234 " pdb="FE4 SF4 E1006 " - pdb=" SG CYS E 188 " pdb="FE1 SF4 E1006 " - pdb=" SG CYS E 185 " pdb=" SF4 E1007 " pdb="FE3 SF4 E1007 " - pdb=" SG CYS E 227 " pdb="FE2 SF4 E1007 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E1007 " - pdb=" SG CYS E 192 " pdb="FE1 SF4 E1007 " - pdb=" SG CYS E 230 " pdb=" SF4 E1008 " pdb="FE2 SF4 E1008 " - pdb=" SG CYS E 293 " pdb="FE4 SF4 E1008 " - pdb=" SG CYS E 265 " pdb="FE1 SF4 E1008 " - pdb=" SG CYS E 258 " pdb="FE3 SF4 E1008 " - pdb=" SG CYS E 261 " pdb=" SF4 F 602 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 433 " pdb="FE3 SF4 F 602 " - pdb=" SG CYS F 430 " pdb="FE4 SF4 F 602 " - pdb=" SG CYS F 427 " pdb="FE1 SF4 F 602 " - pdb=" SG CYS F 471 " Number of angles added : 138 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 30 sheets defined 36.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 12 No H-bonds generated for 'chain 'A' and resid 9 through 12' Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.982A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.611A pdb=" N MET A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.164A pdb=" N ARG A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 388 through 397 removed outlier: 4.040A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.653A pdb=" N ARG A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.750A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 removed outlier: 3.716A pdb=" N GLU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.900A pdb=" N LEU A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 750 through 760 Processing helix chain 'A' and resid 769 through 774 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 859 through 862 No H-bonds generated for 'chain 'A' and resid 859 through 862' Processing helix chain 'A' and resid 940 through 951 Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 67 through 72 Proline residue: B 71 - end of helix No H-bonds generated for 'chain 'B' and resid 67 through 72' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 91 through 94 No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 132 through 141 removed outlier: 3.693A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.804A pdb=" N VAL B 207 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.789A pdb=" N ALA B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 removed outlier: 3.696A pdb=" N GLU B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.363A pdb=" N HIS B 382 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 411 through 424 removed outlier: 3.693A pdb=" N MET B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 436 through 449 removed outlier: 4.024A pdb=" N GLU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 468 Processing helix chain 'B' and resid 477 through 487 removed outlier: 3.971A pdb=" N VAL B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 51 through 60 removed outlier: 3.535A pdb=" N VAL G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 87 through 98 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'D' and resid 5 through 19 removed outlier: 4.385A pdb=" N VAL D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 57 through 65 Proline residue: D 64 - end of helix Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 100 through 116 removed outlier: 3.980A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 138 removed outlier: 3.612A pdb=" N MET E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 242 through 246 removed outlier: 4.164A pdb=" N ARG E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 327 through 345 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 360 through 371 Processing helix chain 'E' and resid 388 through 397 removed outlier: 4.039A pdb=" N LYS E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 428 through 440 removed outlier: 3.653A pdb=" N ARG E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA E 440 " --> pdb=" O LYS E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 492 through 498 Processing helix chain 'E' and resid 502 through 511 removed outlier: 3.750A pdb=" N ASP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 525 removed outlier: 3.716A pdb=" N GLU E 522 " --> pdb=" O PRO E 518 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 541 Processing helix chain 'E' and resid 560 through 573 Processing helix chain 'E' and resid 592 through 597 Processing helix chain 'E' and resid 614 through 624 removed outlier: 3.900A pdb=" N LEU E 619 " --> pdb=" O ALA E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 645 Processing helix chain 'E' and resid 665 through 673 Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 730 through 741 Processing helix chain 'E' and resid 750 through 760 Processing helix chain 'E' and resid 769 through 774 Processing helix chain 'E' and resid 844 through 846 No H-bonds generated for 'chain 'E' and resid 844 through 846' Processing helix chain 'E' and resid 859 through 862 No H-bonds generated for 'chain 'E' and resid 859 through 862' Processing helix chain 'E' and resid 940 through 951 Processing helix chain 'F' and resid 9 through 12 No H-bonds generated for 'chain 'F' and resid 9 through 12' Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 67 through 72 Proline residue: F 71 - end of helix No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 91 through 94 No H-bonds generated for 'chain 'F' and resid 91 through 94' Processing helix chain 'F' and resid 112 through 118 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 132 through 142 removed outlier: 3.694A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 193 through 207 removed outlier: 3.803A pdb=" N VAL F 207 " --> pdb=" O GLY F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.790A pdb=" N ALA F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 removed outlier: 3.696A pdb=" N GLU F 240 " --> pdb=" O PRO F 236 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA F 241 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 259 through 266 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 378 through 382 removed outlier: 4.363A pdb=" N HIS F 382 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 411 through 424 removed outlier: 3.693A pdb=" N MET F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 434 No H-bonds generated for 'chain 'F' and resid 431 through 434' Processing helix chain 'F' and resid 436 through 449 removed outlier: 4.024A pdb=" N GLU F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 468 Processing helix chain 'F' and resid 477 through 487 removed outlier: 3.971A pdb=" N VAL F 481 " --> pdb=" O THR F 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 21 through 31 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.535A pdb=" N VAL C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'H' and resid 5 through 19 removed outlier: 4.384A pdb=" N VAL H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 35 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 57 through 65 Proline residue: H 64 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 24 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= E, first strand: chain 'A' and resid 252 through 257 removed outlier: 3.516A pdb=" N ARG A 278 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 443 through 446 removed outlier: 5.775A pdb=" N GLY A 582 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR A 549 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN A 584 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.218A pdb=" N ILE A 679 " --> pdb=" O VAL A 653 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 706 through 709 Processing sheet with id= I, first strand: chain 'A' and resid 853 through 856 removed outlier: 8.513A pdb=" N LEU A 854 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 884 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 856 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR A 886 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.590A pdb=" N ASP B 35 " --> pdb=" O ILE B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.869A pdb=" N GLY B 85 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.942A pdb=" N TYR B 170 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 172 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG B 211 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N CYS B 173 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR B 213 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU B 244 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL B 214 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU B 246 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 216 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG B 248 " --> pdb=" O ILE B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 323 through 328 Processing sheet with id= N, first strand: chain 'B' and resid 363 through 368 removed outlier: 6.955A pdb=" N HIS B 405 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 366 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 403 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 74 through 76 Processing sheet with id= P, first strand: chain 'E' and resid 24 through 29 Processing sheet with id= Q, first strand: chain 'E' and resid 72 through 74 Processing sheet with id= R, first strand: chain 'E' and resid 175 through 177 Processing sheet with id= S, first strand: chain 'E' and resid 202 through 204 Processing sheet with id= T, first strand: chain 'E' and resid 252 through 257 removed outlier: 3.514A pdb=" N ARG E 278 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU E 272 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 443 through 446 removed outlier: 5.774A pdb=" N GLY E 582 " --> pdb=" O ILE E 547 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR E 549 " --> pdb=" O GLY E 582 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN E 584 " --> pdb=" O TYR E 549 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 652 through 654 removed outlier: 6.218A pdb=" N ILE E 679 " --> pdb=" O VAL E 653 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 706 through 709 Processing sheet with id= X, first strand: chain 'E' and resid 853 through 856 removed outlier: 8.513A pdb=" N LEU E 854 " --> pdb=" O THR E 882 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG E 884 " --> pdb=" O LEU E 854 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE E 856 " --> pdb=" O ARG E 884 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR E 886 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.589A pdb=" N ASP F 35 " --> pdb=" O ILE F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 53 through 55 removed outlier: 3.870A pdb=" N GLY F 85 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.942A pdb=" N TYR F 170 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN F 293 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL F 172 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG F 211 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N CYS F 173 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR F 213 " --> pdb=" O CYS F 173 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU F 244 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL F 214 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU F 246 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE F 216 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG F 248 " --> pdb=" O ILE F 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 323 through 328 Processing sheet with id= AC, first strand: chain 'F' and resid 363 through 368 removed outlier: 6.954A pdb=" N HIS F 405 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL F 366 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 403 " --> pdb=" O VAL F 366 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 74 through 76 702 hydrogen bonds defined for protein. 1968 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: 8.92 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 10625 1.42 - 1.64: 14883 1.64 - 1.85: 276 1.85 - 2.07: 8 2.07 - 2.28: 136 Bond restraints: 25928 Sorted by residual: bond pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " ideal model delta sigma weight residual 1.610 1.852 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " ideal model delta sigma weight residual 1.610 1.852 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O3A MGD E1001 " pdb=" PA MGD E1001 " ideal model delta sigma weight residual 1.649 1.857 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" O3A MGD A1001 " pdb=" PA MGD A1001 " ideal model delta sigma weight residual 1.649 1.857 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" O5' MGD A1001 " pdb=" PB MGD A1001 " ideal model delta sigma weight residual 1.646 1.850 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 25923 not shown) Histogram of bond angle deviations from ideal: 73.27 - 85.46: 128 85.46 - 97.64: 8 97.64 - 109.83: 3776 109.83 - 122.02: 25930 122.02 - 134.20: 5532 Bond angle restraints: 35374 Sorted by residual: angle pdb=" S1 FES C 201 " pdb="FE2 FES C 201 " pdb=" S2 FES C 201 " ideal model delta sigma weight residual 104.33 83.82 20.51 1.14e+00 7.69e-01 3.24e+02 angle pdb=" S1 FES G 201 " pdb="FE2 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.83 20.50 1.14e+00 7.69e-01 3.23e+02 angle pdb=" S1 FES E1004 " pdb="FE2 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 83.85 20.48 1.14e+00 7.69e-01 3.23e+02 angle pdb=" S1 FES A1004 " pdb="FE2 FES A1004 " pdb=" S2 FES A1004 " ideal model delta sigma weight residual 104.33 83.86 20.47 1.14e+00 7.69e-01 3.22e+02 angle pdb=" S1 FES E1004 " pdb="FE1 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 83.84 20.49 1.20e+00 6.94e-01 2.91e+02 ... (remaining 35369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 15119 33.50 - 67.00: 377 67.00 - 100.49: 40 100.49 - 133.99: 0 133.99 - 167.49: 4 Dihedral angle restraints: 15540 sinusoidal: 6146 harmonic: 9394 Sorted by residual: dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 90.10 167.49 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C10 FMN F 601 " pdb=" C1' FMN F 601 " pdb=" N10 FMN F 601 " pdb=" C2' FMN F 601 " ideal model delta sinusoidal sigma weight residual 257.59 90.16 167.43 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' FMN F 601 " pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " pdb=" O1P FMN F 601 " ideal model delta sinusoidal sigma weight residual 75.26 -141.04 -143.70 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 15537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3853 0.098 - 0.195: 71 0.195 - 0.293: 14 0.293 - 0.390: 6 0.390 - 0.488: 8 Chirality restraints: 3952 Sorted by residual: chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL E 385 " pdb=" CA VAL E 385 " pdb=" CG1 VAL E 385 " pdb=" CG2 VAL E 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" C23 MGD A1002 " pdb=" C14 MGD A1002 " pdb=" N22 MGD A1002 " pdb=" O11 MGD A1002 " both_signs ideal model delta sigma weight residual False 2.33 2.78 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 3949 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 773 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASP A 773 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 773 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 774 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 773 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ASP E 773 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP E 773 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA E 774 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 222 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C SER E 222 " -0.034 2.00e-02 2.50e+03 pdb=" O SER E 222 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP E 223 " 0.011 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 179 2.51 - 3.11: 19558 3.11 - 3.70: 38704 3.70 - 4.30: 58418 4.30 - 4.90: 98915 Nonbonded interactions: 215774 Sorted by model distance: nonbonded pdb=" OG1 THR E 882 " pdb=" O PRO E 937 " model vdw 1.909 2.440 nonbonded pdb=" OG1 THR A 882 " pdb=" O PRO A 937 " model vdw 1.909 2.440 nonbonded pdb=" OG1 THR A 817 " pdb=" O PHE A 821 " model vdw 1.988 2.440 nonbonded pdb=" OG1 THR E 817 " pdb=" O PHE E 821 " model vdw 1.988 2.440 nonbonded pdb=" OE1 GLU E 631 " pdb=" NH2 ARG H 41 " model vdw 2.119 2.520 ... (remaining 215769 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.950 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 73.820 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.242 25928 Z= 0.670 Angle : 1.165 20.514 35374 Z= 0.775 Chirality : 0.045 0.488 3952 Planarity : 0.004 0.047 4604 Dihedral : 15.124 167.490 9532 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 1.13 % Allowed : 2.77 % Favored : 96.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: -3.82 (0.12), residues: 3302 helix: -1.96 (0.12), residues: 1286 sheet: -2.99 (0.25), residues: 302 loop : -2.95 (0.12), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 780 HIS 0.006 0.001 HIS A 387 PHE 0.009 0.001 PHE A 175 TYR 0.015 0.001 TYR A 260 ARG 0.003 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 540 time to evaluate : 2.532 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7607 (mtt) cc_final: 0.7392 (mtt) REVERT: A 601 PHE cc_start: 0.7758 (m-80) cc_final: 0.7447 (m-10) REVERT: A 614 ASP cc_start: 0.6502 (m-30) cc_final: 0.5933 (m-30) REVERT: B 179 ASP cc_start: 0.7196 (m-30) cc_final: 0.6895 (m-30) REVERT: B 227 MET cc_start: 0.8407 (tpp) cc_final: 0.7767 (tpt) REVERT: B 445 ASP cc_start: 0.6869 (m-30) cc_final: 0.6534 (m-30) REVERT: E 78 MET cc_start: 0.7611 (mtt) cc_final: 0.7395 (mtt) REVERT: E 601 PHE cc_start: 0.7748 (m-80) cc_final: 0.7483 (m-10) REVERT: E 614 ASP cc_start: 0.6473 (m-30) cc_final: 0.5909 (m-30) REVERT: F 179 ASP cc_start: 0.7194 (m-30) cc_final: 0.6917 (m-30) REVERT: F 227 MET cc_start: 0.8406 (tpp) cc_final: 0.7767 (tpt) REVERT: F 445 ASP cc_start: 0.6867 (m-30) cc_final: 0.6532 (m-30) outliers start: 29 outliers final: 3 residues processed: 567 average time/residue: 0.4423 time to fit residues: 367.8913 Evaluate side-chains 343 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 340 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 892 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 166 optimal weight: 0.0470 chunk 132 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS A 387 HIS A 589 GLN A 690 ASN A 794 HIS A 920 ASN A 930 GLN A 941 GLN G 91 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS E 387 HIS E 589 GLN E 779 GLN E 794 HIS E 920 ASN E 930 GLN E 941 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25928 Z= 0.322 Angle : 0.691 10.906 35374 Z= 0.342 Chirality : 0.046 0.208 3952 Planarity : 0.006 0.077 4604 Dihedral : 10.126 172.951 3891 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 2.27 % Allowed : 11.09 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.48 (0.14), residues: 3302 helix: -0.75 (0.14), residues: 1270 sheet: -2.06 (0.26), residues: 344 loop : -2.29 (0.13), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 780 HIS 0.006 0.001 HIS B 405 PHE 0.022 0.002 PHE A 728 TYR 0.023 0.002 TYR E 260 ARG 0.007 0.001 ARG E 719 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 386 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.6471 (m-30) cc_final: 0.5913 (m-30) REVERT: A 793 MET cc_start: 0.6693 (mmt) cc_final: 0.6235 (ttp) REVERT: E 614 ASP cc_start: 0.6498 (m-30) cc_final: 0.5941 (m-30) REVERT: E 793 MET cc_start: 0.6726 (mmt) cc_final: 0.6047 (mtm) outliers start: 58 outliers final: 32 residues processed: 426 average time/residue: 0.4186 time to fit residues: 266.8817 Evaluate side-chains 356 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 661 SER Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 460 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 264 optimal weight: 0.0370 chunk 294 optimal weight: 4.9990 chunk 101 optimal weight: 0.0870 chunk 237 optimal weight: 4.9990 overall best weight: 1.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN A 920 ASN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 686 ASN E 920 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25928 Z= 0.252 Angle : 0.607 12.484 35374 Z= 0.300 Chirality : 0.043 0.216 3952 Planarity : 0.005 0.079 4604 Dihedral : 9.538 171.060 3890 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.94 % Favored : 94.88 % Rotamer: Outliers : 3.36 % Allowed : 12.46 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.95 (0.14), residues: 3302 helix: -0.38 (0.15), residues: 1290 sheet: -1.82 (0.25), residues: 374 loop : -1.92 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 780 HIS 0.003 0.001 HIS B 405 PHE 0.012 0.001 PHE A 175 TYR 0.022 0.002 TYR A 260 ARG 0.010 0.000 ARG E 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 341 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7324 (mp) REVERT: A 793 MET cc_start: 0.6742 (mmt) cc_final: 0.6374 (ttp) REVERT: B 190 GLU cc_start: 0.6798 (tt0) cc_final: 0.6581 (mt-10) REVERT: B 298 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7269 (mp) REVERT: E 223 ASP cc_start: 0.7999 (m-30) cc_final: 0.7692 (m-30) REVERT: E 405 GLN cc_start: 0.7831 (mp10) cc_final: 0.7422 (mp10) REVERT: E 793 MET cc_start: 0.6703 (mmt) cc_final: 0.6398 (ttp) REVERT: F 190 GLU cc_start: 0.6811 (tt0) cc_final: 0.6585 (mt-10) outliers start: 86 outliers final: 51 residues processed: 410 average time/residue: 0.4304 time to fit residues: 267.9584 Evaluate side-chains 374 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 321 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 367 GLN E 133 GLN E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25928 Z= 0.420 Angle : 0.700 13.584 35374 Z= 0.350 Chirality : 0.048 0.269 3952 Planarity : 0.006 0.082 4604 Dihedral : 9.728 168.207 3890 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 4.53 % Allowed : 13.55 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.06 % 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: -1.93 (0.14), residues: 3302 helix: -0.36 (0.15), residues: 1258 sheet: -1.97 (0.24), residues: 406 loop : -1.82 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 780 HIS 0.006 0.001 HIS E 387 PHE 0.015 0.002 PHE E 208 TYR 0.025 0.002 TYR E 260 ARG 0.015 0.001 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 329 time to evaluate : 2.594 Fit side-chains REVERT: A 223 ASP cc_start: 0.8170 (m-30) cc_final: 0.7836 (m-30) REVERT: A 394 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7314 (mp) REVERT: A 793 MET cc_start: 0.6878 (mmt) cc_final: 0.6498 (ttp) REVERT: B 298 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7355 (mp) REVERT: B 396 LEU cc_start: 0.6277 (tp) cc_final: 0.5754 (mt) REVERT: E 223 ASP cc_start: 0.8166 (m-30) cc_final: 0.7835 (m-30) REVERT: E 405 GLN cc_start: 0.7931 (mp10) cc_final: 0.7453 (mp10) REVERT: E 793 MET cc_start: 0.6837 (mmt) cc_final: 0.6471 (ttp) REVERT: F 190 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: F 396 LEU cc_start: 0.6286 (tp) cc_final: 0.5745 (mt) outliers start: 116 outliers final: 83 residues processed: 417 average time/residue: 0.4195 time to fit residues: 265.0156 Evaluate side-chains 399 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 313 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25928 Z= 0.412 Angle : 0.692 14.829 35374 Z= 0.345 Chirality : 0.048 0.271 3952 Planarity : 0.006 0.087 4604 Dihedral : 9.260 165.232 3890 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Rotamer: Outliers : 4.73 % Allowed : 15.59 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.06 % 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: -1.83 (0.14), residues: 3302 helix: -0.26 (0.15), residues: 1244 sheet: -1.85 (0.26), residues: 390 loop : -1.79 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 780 HIS 0.004 0.001 HIS A 427 PHE 0.017 0.002 PHE E 728 TYR 0.027 0.002 TYR A 260 ARG 0.005 0.001 ARG E 877 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 320 time to evaluate : 2.684 Fit side-chains REVERT: A 223 ASP cc_start: 0.8185 (m-30) cc_final: 0.7928 (m-30) REVERT: A 317 LYS cc_start: 0.7443 (mtmt) cc_final: 0.7195 (mtpt) REVERT: A 394 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7301 (mp) REVERT: A 793 MET cc_start: 0.7002 (mmt) cc_final: 0.6581 (mtm) REVERT: B 298 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7342 (mp) REVERT: B 396 LEU cc_start: 0.6450 (tp) cc_final: 0.5845 (mt) REVERT: G 133 VAL cc_start: 0.8706 (m) cc_final: 0.8502 (t) REVERT: E 223 ASP cc_start: 0.8188 (m-30) cc_final: 0.7834 (m-30) REVERT: E 317 LYS cc_start: 0.7460 (mtmt) cc_final: 0.7203 (mtpt) REVERT: E 405 GLN cc_start: 0.8048 (mp10) cc_final: 0.7585 (mp10) REVERT: E 793 MET cc_start: 0.6917 (mmt) cc_final: 0.6544 (mtm) REVERT: F 159 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6994 (mtp180) REVERT: F 396 LEU cc_start: 0.6472 (tp) cc_final: 0.5810 (mt) REVERT: C 133 VAL cc_start: 0.8708 (m) cc_final: 0.8500 (t) outliers start: 121 outliers final: 88 residues processed: 414 average time/residue: 0.4207 time to fit residues: 266.8049 Evaluate side-chains 393 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 303 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 315 optimal weight: 10.0000 chunk 261 optimal weight: 0.0770 chunk 146 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25928 Z= 0.167 Angle : 0.562 16.745 35374 Z= 0.275 Chirality : 0.041 0.144 3952 Planarity : 0.005 0.087 4604 Dihedral : 8.784 165.581 3890 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 2.70 % Allowed : 18.32 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.14), residues: 3302 helix: 0.22 (0.15), residues: 1230 sheet: -1.48 (0.27), residues: 376 loop : -1.62 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 780 HIS 0.002 0.001 HIS E 152 PHE 0.010 0.001 PHE E 728 TYR 0.019 0.001 TYR E 260 ARG 0.004 0.000 ARG E 719 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 321 time to evaluate : 2.938 Fit side-chains REVERT: A 223 ASP cc_start: 0.8031 (m-30) cc_final: 0.7682 (m-30) REVERT: A 358 CYS cc_start: 0.7473 (m) cc_final: 0.7056 (m) REVERT: A 793 MET cc_start: 0.6864 (mmt) cc_final: 0.6508 (mtm) REVERT: B 45 ILE cc_start: 0.8670 (mm) cc_final: 0.8358 (mm) REVERT: B 298 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7245 (mp) REVERT: B 396 LEU cc_start: 0.6490 (tp) cc_final: 0.5933 (mt) REVERT: E 223 ASP cc_start: 0.8031 (m-30) cc_final: 0.7721 (m-30) REVERT: E 358 CYS cc_start: 0.7463 (m) cc_final: 0.7039 (m) REVERT: E 405 GLN cc_start: 0.7861 (mp10) cc_final: 0.7489 (mp10) REVERT: E 793 MET cc_start: 0.6773 (mmt) cc_final: 0.6473 (mtm) REVERT: F 45 ILE cc_start: 0.8663 (mm) cc_final: 0.8348 (mm) REVERT: F 396 LEU cc_start: 0.6504 (tp) cc_final: 0.5945 (mt) outliers start: 69 outliers final: 51 residues processed: 375 average time/residue: 0.4195 time to fit residues: 236.6347 Evaluate side-chains 356 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 304 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 178 optimal weight: 0.3980 chunk 265 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25928 Z= 0.188 Angle : 0.569 17.161 35374 Z= 0.277 Chirality : 0.041 0.168 3952 Planarity : 0.004 0.068 4604 Dihedral : 8.688 165.432 3888 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 3.36 % Allowed : 18.09 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.15), residues: 3302 helix: 0.41 (0.15), residues: 1222 sheet: -1.28 (0.28), residues: 366 loop : -1.48 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 780 HIS 0.004 0.001 HIS A 603 PHE 0.011 0.001 PHE A 728 TYR 0.019 0.001 TYR E 260 ARG 0.004 0.000 ARG F 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 314 time to evaluate : 2.823 Fit side-chains REVERT: A 223 ASP cc_start: 0.8054 (m-30) cc_final: 0.7716 (m-30) REVERT: A 358 CYS cc_start: 0.7467 (m) cc_final: 0.7031 (m) REVERT: A 793 MET cc_start: 0.6876 (mmt) cc_final: 0.6462 (mtm) REVERT: E 223 ASP cc_start: 0.8055 (m-30) cc_final: 0.7744 (m-30) REVERT: E 358 CYS cc_start: 0.7459 (m) cc_final: 0.7035 (m) REVERT: E 405 GLN cc_start: 0.7887 (mp10) cc_final: 0.7522 (mp10) outliers start: 86 outliers final: 72 residues processed: 384 average time/residue: 0.4226 time to fit residues: 245.3568 Evaluate side-chains 380 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 308 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 483 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 589 GLN ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25928 Z= 0.348 Angle : 0.655 16.408 35374 Z= 0.324 Chirality : 0.046 0.258 3952 Planarity : 0.005 0.072 4604 Dihedral : 8.934 164.880 3888 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 3.75 % Allowed : 18.20 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.28 (0.15), residues: 3302 helix: 0.18 (0.15), residues: 1244 sheet: -1.33 (0.28), residues: 366 loop : -1.52 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 780 HIS 0.021 0.001 HIS E 603 PHE 0.015 0.002 PHE E 728 TYR 0.026 0.002 TYR E 260 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 310 time to evaluate : 2.662 Fit side-chains REVERT: A 223 ASP cc_start: 0.8176 (m-30) cc_final: 0.7854 (m-30) REVERT: A 793 MET cc_start: 0.6929 (mmt) cc_final: 0.6506 (mtm) REVERT: G 133 VAL cc_start: 0.8708 (m) cc_final: 0.8497 (t) REVERT: E 223 ASP cc_start: 0.8166 (m-30) cc_final: 0.7832 (m-30) REVERT: E 358 CYS cc_start: 0.7663 (m) cc_final: 0.7198 (m) REVERT: E 405 GLN cc_start: 0.8000 (mp10) cc_final: 0.7614 (mp10) REVERT: C 133 VAL cc_start: 0.8706 (m) cc_final: 0.8491 (t) outliers start: 96 outliers final: 78 residues processed: 383 average time/residue: 0.4145 time to fit residues: 237.5335 Evaluate side-chains 385 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 307 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 483 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 589 GLN ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25928 Z= 0.331 Angle : 0.648 16.773 35374 Z= 0.321 Chirality : 0.045 0.238 3952 Planarity : 0.005 0.074 4604 Dihedral : 8.927 164.629 3888 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 3.67 % Allowed : 18.75 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3302 helix: 0.14 (0.15), residues: 1246 sheet: -1.34 (0.28), residues: 366 loop : -1.51 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 780 HIS 0.009 0.001 HIS A 603 PHE 0.014 0.002 PHE E 728 TYR 0.024 0.002 TYR A 260 ARG 0.004 0.000 ARG G 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 306 time to evaluate : 2.673 Fit side-chains REVERT: A 223 ASP cc_start: 0.8176 (m-30) cc_final: 0.7851 (m-30) REVERT: A 793 MET cc_start: 0.6902 (mmt) cc_final: 0.6526 (mtm) REVERT: G 133 VAL cc_start: 0.8718 (m) cc_final: 0.8514 (t) REVERT: E 223 ASP cc_start: 0.8160 (m-30) cc_final: 0.7819 (m-30) REVERT: E 405 GLN cc_start: 0.8012 (mp10) cc_final: 0.7630 (mp10) REVERT: E 793 MET cc_start: 0.6927 (mmt) cc_final: 0.6310 (mtm) REVERT: C 133 VAL cc_start: 0.8715 (m) cc_final: 0.8513 (t) outliers start: 94 outliers final: 81 residues processed: 382 average time/residue: 0.4153 time to fit residues: 239.0613 Evaluate side-chains 382 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 301 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 904 ASP Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 483 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 589 GLN ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 HIS ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25928 Z= 0.278 Angle : 0.627 17.103 35374 Z= 0.309 Chirality : 0.044 0.213 3952 Planarity : 0.005 0.078 4604 Dihedral : 8.856 164.586 3888 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 3.59 % Allowed : 18.55 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.17 (0.15), residues: 3302 helix: 0.30 (0.15), residues: 1220 sheet: -1.30 (0.28), residues: 366 loop : -1.46 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 780 HIS 0.018 0.001 HIS A 603 PHE 0.012 0.001 PHE A 728 TYR 0.023 0.002 TYR E 260 ARG 0.004 0.000 ARG G 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 305 time to evaluate : 2.810 Fit side-chains REVERT: A 223 ASP cc_start: 0.8143 (m-30) cc_final: 0.7825 (m-30) REVERT: A 793 MET cc_start: 0.6937 (mmt) cc_final: 0.6524 (mtm) REVERT: B 396 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6210 (tp) REVERT: G 133 VAL cc_start: 0.8705 (m) cc_final: 0.8499 (t) REVERT: E 223 ASP cc_start: 0.8162 (m-30) cc_final: 0.7823 (m-30) REVERT: E 358 CYS cc_start: 0.7639 (m) cc_final: 0.7154 (m) REVERT: E 405 GLN cc_start: 0.7999 (mp10) cc_final: 0.7638 (mp10) REVERT: E 793 MET cc_start: 0.6941 (mmt) cc_final: 0.6324 (mtm) REVERT: F 396 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6214 (tp) REVERT: C 133 VAL cc_start: 0.8699 (m) cc_final: 0.8498 (t) outliers start: 92 outliers final: 86 residues processed: 377 average time/residue: 0.4303 time to fit residues: 244.8910 Evaluate side-chains 392 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 304 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 904 ASP Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 483 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 259 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 534 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS E 534 GLN ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 589 GLN ** E 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 HIS E 716 ASN ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.172771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.147926 restraints weight = 27097.100| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.35 r_work: 0.3417 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25928 Z= 0.263 Angle : 0.617 17.228 35374 Z= 0.304 Chirality : 0.044 0.207 3952 Planarity : 0.005 0.080 4604 Dihedral : 8.816 164.590 3888 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 3.71 % Allowed : 18.55 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.15 (0.15), residues: 3302 helix: 0.30 (0.15), residues: 1232 sheet: -1.23 (0.28), residues: 360 loop : -1.46 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 780 HIS 0.011 0.001 HIS A 603 PHE 0.012 0.001 PHE E 728 TYR 0.023 0.002 TYR E 260 ARG 0.005 0.000 ARG A 877 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5959.45 seconds wall clock time: 107 minutes 29.97 seconds (6449.97 seconds total)