Starting phenix.real_space_refine on Tue Mar 19 22:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/03_2024/6tg9_10495_updated.pdb" } resolution = 3.24 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= 0.001 sd= 0.007 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 14 5.49 5 S 232 5.16 5 C 15818 2.51 5 N 4546 2.21 5 O 4752 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 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 509": "OE1" <-> "OE2" Residue "A GLU 522": "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 GLU 784": "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 GLU 862": "OE1" <-> "OE2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" 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 137": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" 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 GLU 388": "OE1" <-> "OE2" 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 GLU 107": "OE1" <-> "OE2" 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 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 509": "OE1" <-> "OE2" Residue "E GLU 522": "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 GLU 784": "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 GLU 862": "OE1" <-> "OE2" Residue "E ARG 873": "NH1" <-> "NH2" Residue "E ARG 953": "NH1" <-> "NH2" Residue "E GLU 955": "OE1" <-> "OE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" 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 137": "OE1" <-> "OE2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ARG 211": "NH1" <-> "NH2" 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 GLU 388": "OE1" <-> "OE2" 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 GLU 107": "OE1" <-> "OE2" 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25412 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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 386 117.182 70.640 77.272 1.00 7.54 S ATOM 368 SG CYS A 57 89.637 94.653 56.321 1.00 3.56 S ATOM 442 SG CYS A 68 85.866 95.047 55.342 1.00 3.19 S ATOM 467 SG CYS A 71 85.021 98.459 59.082 1.00 6.31 S ATOM 568 SG CYS A 85 88.693 99.076 59.391 1.00 7.88 S ATOM 909 SG CYS A 130 84.111 81.763 52.937 1.00 3.17 S ATOM 852 SG CYS A 121 79.595 79.452 48.578 1.00 16.27 S ATOM 873 SG CYS A 124 85.380 76.133 49.472 1.00 4.70 S ATOM 1347 SG CYS A 185 91.443 88.462 53.256 1.00 4.93 S ATOM 1326 SG CYS A 182 93.268 86.268 47.471 1.00 5.76 S ATOM 1698 SG CYS A 234 92.098 82.196 52.783 1.00 16.27 S ATOM 1372 SG CYS A 188 97.400 86.449 52.275 1.00 5.12 S ATOM 1671 SG CYS A 230 99.486 80.178 55.402 1.00 6.94 S ATOM 1637 SG CYS A 224 104.914 78.460 54.122 1.00 7.72 S ATOM 1656 SG CYS A 227 103.209 80.005 60.480 1.00 16.27 S ATOM 1401 SG CYS A 192 104.854 84.620 56.440 1.00 3.35 S ATOM 1879 SG CYS A 258 103.168 70.723 70.038 1.00 5.48 S ATOM 2135 SG CYS A 293 105.565 73.915 65.834 1.00 16.27 S ATOM 1902 SG CYS A 261 108.688 74.919 71.417 1.00 5.21 S ATOM 1923 SG CYS A 265 103.038 77.511 70.955 1.00 5.41 S ATOM 10736 SG CYS B 471 92.222 106.680 46.250 1.00 7.07 S ATOM 10464 SG CYS B 433 90.747 101.868 42.412 1.00 3.44 S ATOM 10444 SG CYS B 430 89.010 101.057 48.203 1.00 3.21 S ATOM 10427 SG CYS B 427 95.285 100.838 46.917 1.00 4.74 S ATOM 11482 SG CYS G 77 99.187 111.666 27.782 1.00 19.46 S ATOM 11518 SG CYS G 82 98.825 114.152 25.823 1.00 19.75 S ATOM 11763 SG CYS G 116 100.317 114.663 31.851 1.00 17.51 S ATOM 11789 SG CYS G 120 98.921 117.866 30.579 1.00 20.46 S ATOM 15362 SG CYS E 386 36.893 85.570 77.274 1.00 7.46 S ATOM 12855 SG CYS E 57 64.443 61.567 56.321 1.00 3.83 S ATOM 12929 SG CYS E 68 68.208 61.173 55.344 1.00 3.38 S ATOM 12954 SG CYS E 71 69.060 57.758 59.086 1.00 6.44 S ATOM 13055 SG CYS E 85 65.383 57.136 59.392 1.00 8.09 S ATOM 13396 SG CYS E 130 69.963 74.450 52.937 1.00 4.11 S ATOM 13339 SG CYS E 121 74.479 76.761 48.578 1.00 6.47 S ATOM 13360 SG CYS E 124 68.694 80.079 49.472 1.00 3.69 S ATOM 13834 SG CYS E 185 62.632 67.750 53.257 1.00 3.95 S ATOM 13813 SG CYS E 182 60.806 69.944 47.472 1.00 5.85 S ATOM 14185 SG CYS E 234 61.977 74.016 52.784 1.00 16.27 S ATOM 13859 SG CYS E 188 56.674 69.763 52.276 1.00 6.15 S ATOM 14158 SG CYS E 230 54.588 76.033 55.404 1.00 6.85 S ATOM 14124 SG CYS E 224 49.160 77.751 54.124 1.00 7.97 S ATOM 14143 SG CYS E 227 50.866 76.206 60.482 1.00 7.86 S ATOM 13888 SG CYS E 192 49.221 71.591 56.442 1.00 4.36 S ATOM 14366 SG CYS E 258 50.906 85.488 70.040 1.00 5.53 S ATOM 14622 SG CYS E 293 48.509 82.296 65.836 1.00 16.27 S ATOM 14389 SG CYS E 261 45.387 81.292 71.419 1.00 5.15 S ATOM 14410 SG CYS E 265 51.037 78.700 70.957 1.00 5.57 S ATOM 23223 SG CYS F 471 61.854 49.532 46.251 1.00 7.06 S ATOM 22951 SG CYS F 433 63.329 54.344 42.413 1.00 3.42 S ATOM 22931 SG CYS F 430 65.066 55.156 48.205 1.00 3.20 S ATOM 22914 SG CYS F 427 58.791 55.373 46.919 1.00 4.74 S ATOM 23969 SG CYS C 77 55.046 44.537 27.849 1.00 19.85 S ATOM 24005 SG CYS C 82 55.411 42.045 25.897 1.00 19.67 S ATOM 24250 SG CYS C 116 53.871 41.553 31.915 1.00 17.79 S ATOM 24276 SG CYS C 120 55.261 38.341 30.660 1.00 20.77 S Time building chain proxies: 13.04, per 1000 atoms: 0.51 Number of scatterers: 25412 At special positions: 0 Unit cell: (155.15, 157.29, 116.63, 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 14 15.00 O 4752 8.00 N 4546 7.00 C 15818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.75 Conformation dependent library (CDL) restraints added in 4.2 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 85 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 71 " 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 120 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 116 " pdb=" FES E1004 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 68 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 85 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 57 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 71 " 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 120 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 116 " 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="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 188 " pdb=" SF4 A1007 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb=" SF4 B 602 " 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="FE2 SF4 B 602 " - pdb=" SG CYS B 433 " 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="FE1 SF4 E1006 " - pdb=" SG CYS E 185 " pdb="FE4 SF4 E1006 " - pdb=" SG CYS E 188 " pdb=" SF4 E1007 " pdb="FE2 SF4 E1007 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E1007 " - pdb=" SG CYS E 192 " pdb="FE3 SF4 E1007 " - pdb=" SG CYS E 227 " pdb="FE1 SF4 E1007 " - pdb=" SG CYS E 230 " pdb=" SF4 E1008 " pdb="FE2 SF4 E1008 " - pdb=" SG CYS E 293 " pdb="FE3 SF4 E1008 " - pdb=" SG CYS E 261 " pdb="FE4 SF4 E1008 " - pdb=" SG CYS E 265 " pdb="FE1 SF4 E1008 " - pdb=" SG CYS E 258 " pdb=" SF4 F 602 " 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 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 433 " 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 28 sheets defined 35.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 42 through 48 Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.831A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 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 229 through 233 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 327 through 344 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 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 389 through 397 removed outlier: 4.200A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 412 Processing helix chain 'A' and resid 428 through 438 removed outlier: 3.712A pdb=" N ARG A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 437 " --> pdb=" O ARG A 433 " (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: 3.774A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 518 through 525 removed outlier: 5.450A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.493A 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 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' 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: 3.632A 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 687 through 691 removed outlier: 3.551A pdb=" N ASN A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) 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 775 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 949 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 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 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 117 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.713A pdb=" N SER B 142 " --> pdb=" O GLU B 138 " (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 194 through 207 Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 235 through 241 removed outlier: 3.628A pdb=" N GLU B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) removed outlier: 4.490A 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 295 through 307 removed outlier: 4.003A pdb=" N VAL B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix 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: 4.359A 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: 3.689A pdb=" N MET B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 449 removed outlier: 3.945A pdb=" N GLY B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.134A 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 32 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 Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 87 through 97 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'D' and resid 5 through 18 Processing helix chain 'D' and resid 26 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 42 through 48 Processing helix chain 'E' and resid 100 through 116 removed outlier: 3.831A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 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 229 through 233 Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 294 through 297 No H-bonds generated for 'chain 'E' and resid 294 through 297' Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 327 through 344 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 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 389 through 397 removed outlier: 4.199A pdb=" N LYS E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 412 Processing helix chain 'E' and resid 428 through 438 removed outlier: 3.713A pdb=" N ARG E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG E 437 " --> pdb=" O ARG E 433 " (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: 3.773A pdb=" N ASP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 516 No H-bonds generated for 'chain 'E' and resid 514 through 516' Processing helix chain 'E' and resid 518 through 525 removed outlier: 5.450A pdb=" N SER E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 4.494A 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 551 through 554 No H-bonds generated for 'chain 'E' and resid 551 through 554' 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: 3.632A 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 687 through 691 removed outlier: 3.551A pdb=" N ASN E 690 " --> pdb=" O GLU E 687 " (cutoff:3.500A) 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 775 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 949 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 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 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 117 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 134 through 142 removed outlier: 3.712A 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 194 through 207 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 235 through 241 removed outlier: 3.627A pdb=" N GLU F 240 " --> pdb=" O PRO F 236 " (cutoff:3.500A) removed outlier: 4.490A 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 295 through 307 removed outlier: 4.001A pdb=" N VAL F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Proline residue: F 302 - end of helix 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: 4.361A 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: 3.689A pdb=" N MET F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 449 removed outlier: 3.945A pdb=" N GLY F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 437 " --> pdb=" O CYS F 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.134A 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 32 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 Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 26 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 25 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= D, first strand: chain 'A' and resid 252 through 257 removed outlier: 3.622A pdb=" N ARG A 278 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 582 through 585 removed outlier: 3.878A pdb=" N GLY A 582 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 415 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N TYR A 548 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 417 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS A 443 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 418 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 445 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.383A pdb=" N ILE A 679 " --> pdb=" O VAL A 653 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 706 through 709 Processing sheet with id= H, first strand: chain 'A' and resid 826 through 828 Processing sheet with id= I, first strand: chain 'A' and resid 853 through 856 removed outlier: 8.700A pdb=" N LEU A 854 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG A 884 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE A 856 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A 886 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 35 through 37 removed outlier: 5.450A pdb=" N LYS B 2 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 54 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 52 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 51 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 62 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 85 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.872A pdb=" N TYR B 170 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN B 293 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 172 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 7.122A 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: 7.075A pdb=" N TYR B 213 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU B 244 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL B 214 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 246 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 216 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG B 248 " --> pdb=" O ILE B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 323 through 328 Processing sheet with id= M, first strand: chain 'B' and resid 363 through 368 removed outlier: 7.005A pdb=" N HIS B 405 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 366 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 403 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 74 through 76 Processing sheet with id= O, first strand: chain 'E' and resid 25 through 29 Processing sheet with id= P, first strand: chain 'E' and resid 175 through 177 Processing sheet with id= Q, first strand: chain 'E' and resid 202 through 204 Processing sheet with id= R, first strand: chain 'E' and resid 252 through 257 removed outlier: 3.623A pdb=" N ARG E 278 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 272 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 582 through 585 removed outlier: 3.877A pdb=" N GLY E 582 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU E 415 " --> pdb=" O ALA E 546 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR E 548 " --> pdb=" O LEU E 415 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 417 " --> pdb=" O TYR E 548 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS E 443 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL E 418 " --> pdb=" O LYS E 443 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE E 445 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 652 through 654 removed outlier: 6.383A pdb=" N ILE E 679 " --> pdb=" O VAL E 653 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 706 through 709 Processing sheet with id= V, first strand: chain 'E' and resid 826 through 828 Processing sheet with id= W, first strand: chain 'E' and resid 853 through 856 removed outlier: 8.700A pdb=" N LEU E 854 " --> pdb=" O THR E 882 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG E 884 " --> pdb=" O LEU E 854 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE E 856 " --> pdb=" O ARG E 884 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR E 886 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 35 through 37 removed outlier: 5.451A pdb=" N LYS F 2 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 54 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 52 " --> pdb=" O TRP F 4 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU F 51 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE F 62 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY F 85 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.872A pdb=" N TYR F 170 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN F 293 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 172 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG F 211 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N CYS F 173 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR F 213 " --> pdb=" O CYS F 173 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU F 244 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL F 214 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU F 246 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE F 216 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG F 248 " --> pdb=" O ILE F 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 323 through 328 Processing sheet with id= AA, first strand: chain 'F' and resid 363 through 368 removed outlier: 7.005A pdb=" N HIS F 405 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL F 366 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 403 " --> pdb=" O VAL F 366 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 74 through 76 708 hydrogen bonds defined for protein. 2040 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: 8.60 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 10681 1.42 - 1.64: 14919 1.64 - 1.85: 286 1.85 - 2.07: 2 2.07 - 2.28: 136 Bond restraints: 26024 Sorted by residual: bond pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " ideal model delta sigma weight residual 1.610 1.842 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " ideal model delta sigma weight residual 1.610 1.842 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" O3A MGD E1001 " pdb=" PA MGD E1001 " ideal model delta sigma weight residual 1.649 1.858 -0.209 2.00e-02 2.50e+03 1.09e+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=" O3A MGD E1002 " pdb=" PA MGD E1002 " ideal model delta sigma weight residual 1.649 1.851 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 26019 not shown) Histogram of bond angle deviations from ideal: 73.06 - 85.48: 128 85.48 - 97.90: 12 97.90 - 110.32: 7732 110.32 - 122.74: 23311 122.74 - 135.16: 4337 Bond angle restraints: 35520 Sorted by residual: angle pdb=" S1 FES G 201 " pdb="FE2 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.44 20.89 1.14e+00 7.69e-01 3.36e+02 angle pdb=" S1 FES C 201 " pdb="FE2 FES C 201 " pdb=" S2 FES C 201 " ideal model delta sigma weight residual 104.33 83.46 20.87 1.14e+00 7.69e-01 3.35e+02 angle pdb=" S1 FES G 201 " pdb="FE1 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.41 20.92 1.20e+00 6.94e-01 3.04e+02 angle pdb=" S1 FES E1004 " pdb="FE2 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 84.46 19.87 1.14e+00 7.69e-01 3.04e+02 angle pdb=" S1 FES A1004 " pdb="FE2 FES A1004 " pdb=" S2 FES A1004 " ideal model delta sigma weight residual 104.33 84.47 19.86 1.14e+00 7.69e-01 3.03e+02 ... (remaining 35515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 15283 34.50 - 69.00: 339 69.00 - 103.50: 36 103.50 - 137.99: 2 137.99 - 172.49: 2 Dihedral angle restraints: 15662 sinusoidal: 6268 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 85.10 172.49 1 2.00e+01 2.50e-03 4.78e+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 85.12 172.47 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' FMN B 601 " pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " pdb=" O1P FMN B 601 " ideal model delta sinusoidal sigma weight residual 75.26 -59.96 135.22 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 15659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3499 0.087 - 0.173: 407 0.173 - 0.260: 47 0.260 - 0.347: 11 0.347 - 0.433: 4 Chirality restraints: 3968 Sorted by residual: chirality pdb=" C14 MGD A1002 " pdb=" C13 MGD A1002 " pdb=" C23 MGD A1002 " pdb=" N15 MGD A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C14 MGD E1002 " pdb=" C13 MGD E1002 " pdb=" C23 MGD E1002 " pdb=" N15 MGD E1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C23 MGD E1002 " pdb=" C14 MGD E1002 " pdb=" N22 MGD E1002 " pdb=" O11 MGD E1002 " both_signs ideal model delta sigma weight residual False 2.33 2.75 -0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 3965 not shown) Planarity restraints: 4610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 477 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 478 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 477 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO F 478 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 478 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 478 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 280 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 281 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.024 5.00e-02 4.00e+02 ... (remaining 4607 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 190 2.46 - 3.07: 18610 3.07 - 3.68: 38862 3.68 - 4.29: 58844 4.29 - 4.90: 101462 Nonbonded interactions: 217968 Sorted by model distance: nonbonded pdb=" OG1 THR E 882 " pdb=" O PRO E 937 " model vdw 1.847 2.440 nonbonded pdb=" OG1 THR A 882 " pdb=" O PRO A 937 " model vdw 1.848 2.440 nonbonded pdb=" OG1 THR F 357 " pdb=" O ARG F 361 " model vdw 2.015 2.440 nonbonded pdb=" OG1 THR B 357 " pdb=" O ARG B 361 " model vdw 2.016 2.440 nonbonded pdb=" O LYS E 395 " pdb=" NH2 ARG E 800 " model vdw 2.019 2.520 ... (remaining 217963 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: 0.600 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: 3.540 Check model and map are aligned: 0.380 Set scattering table: 0.200 Process input model: 71.490 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.230 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.016 0.232 26024 Z= 1.034 Angle : 1.327 20.920 35520 Z= 0.890 Chirality : 0.062 0.433 3968 Planarity : 0.004 0.049 4610 Dihedral : 15.198 172.492 9654 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 0.62 % Allowed : 5.39 % Favored : 93.98 % 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: -4.02 (0.12), residues: 3302 helix: -2.11 (0.12), residues: 1246 sheet: -3.07 (0.23), residues: 344 loop : -3.06 (0.12), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 11 HIS 0.010 0.002 HIS E 603 PHE 0.014 0.002 PHE A 407 TYR 0.020 0.002 TYR A 260 ARG 0.012 0.001 ARG A 713 *********************** 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 591 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 575 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8469 (m-10) cc_final: 0.8219 (m-80) REVERT: A 209 ASP cc_start: 0.7466 (t0) cc_final: 0.7006 (t0) REVERT: A 328 THR cc_start: 0.7645 (m) cc_final: 0.7267 (m) REVERT: A 501 TRP cc_start: 0.7047 (t-100) cc_final: 0.6383 (t-100) REVERT: A 728 PHE cc_start: 0.7192 (m-80) cc_final: 0.6837 (m-10) REVERT: B 170 TYR cc_start: 0.7894 (m-80) cc_final: 0.7672 (m-80) REVERT: B 349 LEU cc_start: 0.8126 (tp) cc_final: 0.7875 (tp) REVERT: G 136 LEU cc_start: 0.7194 (mp) cc_final: 0.6993 (mt) REVERT: E 199 PHE cc_start: 0.8464 (m-10) cc_final: 0.8239 (m-10) REVERT: E 209 ASP cc_start: 0.7471 (t0) cc_final: 0.7020 (t0) REVERT: E 328 THR cc_start: 0.7658 (m) cc_final: 0.7278 (m) REVERT: E 501 TRP cc_start: 0.6979 (t-100) cc_final: 0.6349 (t-100) REVERT: E 728 PHE cc_start: 0.7221 (m-80) cc_final: 0.6840 (m-10) REVERT: F 349 LEU cc_start: 0.8116 (tp) cc_final: 0.7873 (tp) REVERT: C 115 TYR cc_start: 0.7783 (m-80) cc_final: 0.7506 (m-80) outliers start: 16 outliers final: 2 residues processed: 589 average time/residue: 0.4473 time to fit residues: 384.1155 Evaluate side-chains 364 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain E residue 12 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 405 GLN A 534 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS E 275 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26024 Z= 0.203 Angle : 0.625 9.732 35520 Z= 0.306 Chirality : 0.043 0.219 3968 Planarity : 0.005 0.049 4610 Dihedral : 10.424 176.206 4012 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.42 % Favored : 95.34 % Rotamer: Outliers : 1.76 % Allowed : 11.48 % Favored : 86.76 % 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: -2.51 (0.14), residues: 3302 helix: -0.64 (0.14), residues: 1260 sheet: -2.61 (0.24), residues: 340 loop : -2.29 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 780 HIS 0.009 0.001 HIS A 901 PHE 0.015 0.001 PHE E 333 TYR 0.015 0.001 TYR A 260 ARG 0.007 0.001 ARG E 666 *********************** 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 464 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 419 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7407 (t0) cc_final: 0.7015 (t0) REVERT: A 501 TRP cc_start: 0.6980 (t-100) cc_final: 0.6434 (t-100) REVERT: A 728 PHE cc_start: 0.6849 (m-80) cc_final: 0.6395 (m-10) REVERT: B 233 MET cc_start: 0.7197 (mtp) cc_final: 0.6946 (mtp) REVERT: E 60 ASP cc_start: 0.7776 (m-30) cc_final: 0.7462 (m-30) REVERT: E 209 ASP cc_start: 0.7420 (t0) cc_final: 0.7049 (t0) REVERT: E 501 TRP cc_start: 0.7000 (t-100) cc_final: 0.6480 (t-100) REVERT: E 728 PHE cc_start: 0.6880 (m-80) cc_final: 0.6444 (m-10) REVERT: F 233 MET cc_start: 0.7199 (mtp) cc_final: 0.6904 (mtp) REVERT: C 115 TYR cc_start: 0.7518 (m-80) cc_final: 0.7048 (m-80) REVERT: C 148 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7153 (mp) outliers start: 45 outliers final: 26 residues processed: 449 average time/residue: 0.3995 time to fit residues: 273.7492 Evaluate side-chains 377 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 350 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 814 ASP Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 320 optimal weight: 0.2980 chunk 264 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS E 275 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26024 Z= 0.297 Angle : 0.624 8.526 35520 Z= 0.307 Chirality : 0.044 0.201 3968 Planarity : 0.005 0.054 4610 Dihedral : 9.640 172.648 4010 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 3.01 % Allowed : 13.09 % Favored : 83.91 % 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: -1.94 (0.14), residues: 3302 helix: -0.21 (0.15), residues: 1266 sheet: -1.97 (0.25), residues: 386 loop : -1.99 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 780 HIS 0.007 0.001 HIS A 901 PHE 0.015 0.001 PHE E 333 TYR 0.020 0.002 TYR A 260 ARG 0.008 0.000 ARG C 101 *********************** 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 444 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 367 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7549 (t0) cc_final: 0.7114 (t0) REVERT: A 501 TRP cc_start: 0.7051 (t-100) cc_final: 0.6399 (t-100) REVERT: B 47 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6246 (pp) REVERT: E 209 ASP cc_start: 0.7555 (t0) cc_final: 0.7132 (t0) REVERT: E 501 TRP cc_start: 0.7046 (t-100) cc_final: 0.6402 (t-100) REVERT: F 47 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6242 (pp) REVERT: C 115 TYR cc_start: 0.7913 (m-80) cc_final: 0.7577 (m-80) outliers start: 77 outliers final: 48 residues processed: 428 average time/residue: 0.3868 time to fit residues: 256.5781 Evaluate side-chains 381 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 331 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 814 ASP Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER 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: 7.9990 chunk 222 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS A 941 GLN E 133 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 941 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 26024 Z= 0.573 Angle : 0.784 13.024 35520 Z= 0.390 Chirality : 0.052 0.259 3968 Planarity : 0.006 0.083 4610 Dihedral : 9.804 166.762 4010 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 3.87 % Allowed : 14.88 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.02 (0.14), residues: 3302 helix: -0.48 (0.14), residues: 1258 sheet: -1.77 (0.27), residues: 378 loop : -1.91 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 501 HIS 0.007 0.002 HIS A 794 PHE 0.016 0.002 PHE A 333 TYR 0.021 0.003 TYR E 260 ARG 0.009 0.001 ARG C 101 *********************** 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 455 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 356 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7733 (t0) cc_final: 0.7279 (t0) REVERT: A 374 PHE cc_start: 0.7895 (m-10) cc_final: 0.7643 (m-10) REVERT: B 47 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6353 (pp) REVERT: B 411 MET cc_start: 0.8027 (mmt) cc_final: 0.7801 (mmt) REVERT: E 209 ASP cc_start: 0.7726 (t0) cc_final: 0.7289 (t0) REVERT: E 374 PHE cc_start: 0.7893 (m-10) cc_final: 0.7635 (m-10) REVERT: F 47 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6356 (pp) REVERT: F 411 MET cc_start: 0.7960 (mmt) cc_final: 0.7699 (mmt) outliers start: 99 outliers final: 72 residues processed: 437 average time/residue: 0.3975 time to fit residues: 267.4303 Evaluate side-chains 409 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 589 GLN Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER 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: 5.9990 chunk 4 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 268 optimal weight: 9.9990 chunk 217 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26024 Z= 0.331 Angle : 0.651 9.362 35520 Z= 0.320 Chirality : 0.045 0.216 3968 Planarity : 0.005 0.057 4610 Dihedral : 9.452 167.612 4010 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.51 % Favored : 94.37 % Rotamer: Outliers : 3.83 % Allowed : 15.86 % Favored : 80.31 % 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: -1.73 (0.14), residues: 3302 helix: -0.27 (0.14), residues: 1270 sheet: -1.56 (0.27), residues: 366 loop : -1.74 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 780 HIS 0.005 0.001 HIS E 291 PHE 0.016 0.001 PHE E 333 TYR 0.021 0.002 TYR A 260 ARG 0.010 0.000 ARG C 101 *********************** 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 438 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 340 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7662 (t0) cc_final: 0.7233 (t0) REVERT: B 47 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6246 (pp) REVERT: B 177 GLU cc_start: 0.7799 (pt0) cc_final: 0.7468 (mt-10) REVERT: B 185 ASP cc_start: 0.6948 (m-30) cc_final: 0.6444 (m-30) REVERT: B 411 MET cc_start: 0.7975 (mmt) cc_final: 0.7708 (mmt) REVERT: E 209 ASP cc_start: 0.7647 (t0) cc_final: 0.7247 (t0) REVERT: E 374 PHE cc_start: 0.7821 (m-10) cc_final: 0.7533 (m-10) REVERT: F 47 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6283 (pp) REVERT: F 263 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8579 (pp) REVERT: F 411 MET cc_start: 0.7910 (mmt) cc_final: 0.7635 (mmp) REVERT: H 67 ARG cc_start: 0.7126 (ptm160) cc_final: 0.6907 (ptm160) outliers start: 98 outliers final: 74 residues processed: 416 average time/residue: 0.3920 time to fit residues: 250.5715 Evaluate side-chains 399 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 322 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN E 930 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26024 Z= 0.292 Angle : 0.624 8.436 35520 Z= 0.306 Chirality : 0.044 0.198 3968 Planarity : 0.005 0.057 4610 Dihedral : 9.295 170.067 4010 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 3.91 % Allowed : 17.19 % Favored : 78.91 % 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: -1.52 (0.14), residues: 3302 helix: -0.07 (0.15), residues: 1268 sheet: -1.48 (0.27), residues: 378 loop : -1.63 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 780 HIS 0.005 0.001 HIS E 610 PHE 0.016 0.001 PHE A 333 TYR 0.019 0.002 TYR A 260 ARG 0.011 0.000 ARG C 101 *********************** 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 443 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 343 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7672 (t0) cc_final: 0.7186 (t0) REVERT: B 47 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6103 (pp) REVERT: B 411 MET cc_start: 0.7987 (mmt) cc_final: 0.7745 (mmp) REVERT: E 209 ASP cc_start: 0.7666 (t0) cc_final: 0.7192 (t0) REVERT: E 374 PHE cc_start: 0.7846 (m-10) cc_final: 0.7544 (m-10) REVERT: F 47 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6124 (pp) REVERT: F 263 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8559 (pp) REVERT: F 411 MET cc_start: 0.7936 (mmt) cc_final: 0.7657 (mmp) outliers start: 100 outliers final: 84 residues processed: 419 average time/residue: 0.4034 time to fit residues: 260.5531 Evaluate side-chains 416 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 329 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 307 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 26024 Z= 0.408 Angle : 0.680 10.961 35520 Z= 0.335 Chirality : 0.047 0.228 3968 Planarity : 0.005 0.061 4610 Dihedral : 9.416 171.272 4010 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.33 % Favored : 93.55 % Rotamer: Outliers : 4.45 % Allowed : 18.24 % Favored : 77.30 % 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: -1.54 (0.14), residues: 3302 helix: -0.10 (0.15), residues: 1270 sheet: -1.45 (0.27), residues: 378 loop : -1.64 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 780 HIS 0.005 0.001 HIS E 610 PHE 0.022 0.002 PHE E 510 TYR 0.021 0.002 TYR A 260 ARG 0.012 0.001 ARG E 622 *********************** 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 457 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 343 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7741 (t0) cc_final: 0.7287 (t0) REVERT: B 47 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6337 (pp) REVERT: B 262 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 411 MET cc_start: 0.8020 (mmt) cc_final: 0.7799 (mmt) REVERT: E 209 ASP cc_start: 0.7719 (t0) cc_final: 0.7307 (t0) REVERT: E 374 PHE cc_start: 0.7888 (m-10) cc_final: 0.7620 (m-10) REVERT: F 47 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6293 (pp) REVERT: F 262 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8239 (tp) REVERT: F 263 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8554 (pp) REVERT: F 411 MET cc_start: 0.7982 (mmt) cc_final: 0.7734 (mmp) outliers start: 114 outliers final: 91 residues processed: 432 average time/residue: 0.3938 time to fit residues: 262.6242 Evaluate side-chains 426 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 330 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 793 MET Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 9.9990 chunk 125 optimal weight: 0.1980 chunk 187 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 794 HIS B 293 ASN B 307 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN F 293 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26024 Z= 0.281 Angle : 0.621 8.444 35520 Z= 0.305 Chirality : 0.044 0.191 3968 Planarity : 0.005 0.057 4610 Dihedral : 9.218 173.899 4010 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 4.10 % Allowed : 18.32 % 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: -1.38 (0.14), residues: 3302 helix: 0.01 (0.15), residues: 1284 sheet: -1.42 (0.27), residues: 378 loop : -1.52 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 780 HIS 0.004 0.001 HIS A 610 PHE 0.015 0.001 PHE E 333 TYR 0.019 0.002 TYR A 260 ARG 0.013 0.000 ARG E 622 *********************** 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 454 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 349 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7688 (t0) cc_final: 0.7186 (t0) REVERT: B 47 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6168 (pp) REVERT: B 262 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 411 MET cc_start: 0.8058 (mmt) cc_final: 0.7812 (mmp) REVERT: E 209 ASP cc_start: 0.7672 (t0) cc_final: 0.7198 (t0) REVERT: F 47 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6178 (pp) REVERT: F 262 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8179 (tp) REVERT: F 263 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (pp) REVERT: F 411 MET cc_start: 0.8007 (mmt) cc_final: 0.7769 (mmp) outliers start: 105 outliers final: 90 residues processed: 428 average time/residue: 0.3999 time to fit residues: 264.6550 Evaluate side-chains 425 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 330 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER 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: 8.9990 chunk 274 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN E 96 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 26024 Z= 0.489 Angle : 0.725 12.014 35520 Z= 0.360 Chirality : 0.049 0.235 3968 Planarity : 0.006 0.075 4610 Dihedral : 9.465 174.056 4010 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 4.06 % Allowed : 18.44 % Favored : 77.50 % 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: -1.55 (0.14), residues: 3302 helix: -0.17 (0.14), residues: 1274 sheet: -1.51 (0.27), residues: 374 loop : -1.59 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.005 0.001 HIS E 610 PHE 0.027 0.002 PHE E 510 TYR 0.023 0.002 TYR G 115 ARG 0.012 0.001 ARG E 622 *********************** 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 435 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 331 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7771 (t0) cc_final: 0.7312 (t0) REVERT: B 47 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6380 (pp) REVERT: B 262 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 411 MET cc_start: 0.8087 (mmt) cc_final: 0.7849 (mmt) REVERT: E 209 ASP cc_start: 0.7761 (t0) cc_final: 0.7327 (t0) REVERT: E 374 PHE cc_start: 0.8019 (m-10) cc_final: 0.7718 (m-10) REVERT: F 47 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6387 (pp) REVERT: F 262 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8243 (tp) REVERT: F 263 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (pp) REVERT: F 411 MET cc_start: 0.8069 (mmt) cc_final: 0.7799 (mmt) outliers start: 104 outliers final: 92 residues processed: 413 average time/residue: 0.3884 time to fit residues: 247.7681 Evaluate side-chains 418 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 321 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 485 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 0.1980 chunk 192 optimal weight: 0.6980 chunk 309 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 258 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 307 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26024 Z= 0.210 Angle : 0.594 7.531 35520 Z= 0.292 Chirality : 0.042 0.172 3968 Planarity : 0.005 0.056 4610 Dihedral : 9.042 173.985 4010 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 3.36 % Allowed : 19.30 % Favored : 77.34 % 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: -1.24 (0.14), residues: 3302 helix: 0.13 (0.15), residues: 1282 sheet: -1.37 (0.27), residues: 374 loop : -1.44 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 780 HIS 0.007 0.001 HIS E 610 PHE 0.015 0.001 PHE A 333 TYR 0.017 0.001 TYR F 215 ARG 0.014 0.000 ARG A 622 ********************** 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 419 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 333 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7673 (t0) cc_final: 0.7195 (t0) REVERT: B 47 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6121 (pp) REVERT: B 262 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8143 (tp) REVERT: E 15 MET cc_start: 0.7414 (mmm) cc_final: 0.7147 (mmm) REVERT: E 209 ASP cc_start: 0.7663 (t0) cc_final: 0.7210 (t0) REVERT: F 47 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6137 (pp) REVERT: F 262 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8115 (tp) outliers start: 86 outliers final: 76 residues processed: 399 average time/residue: 0.3834 time to fit residues: 236.6551 Evaluate side-chains 400 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 320 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 238 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 307 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122684 restraints weight = 32740.088| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.90 r_work: 0.3170 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26024 Z= 0.395 Angle : 0.678 10.619 35520 Z= 0.335 Chirality : 0.047 0.223 3968 Planarity : 0.005 0.059 4610 Dihedral : 9.280 173.978 4010 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer: Outliers : 3.75 % Allowed : 19.26 % Favored : 76.99 % 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 (0.14), residues: 3302 helix: 0.04 (0.15), residues: 1270 sheet: -1.46 (0.27), residues: 374 loop : -1.39 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 780 HIS 0.006 0.001 HIS E 610 PHE 0.015 0.002 PHE E 333 TYR 0.022 0.002 TYR A 260 ARG 0.013 0.001 ARG E 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5799.44 seconds wall clock time: 105 minutes 0.38 seconds (6300.38 seconds total)