Starting phenix.real_space_refine (version: dev) on Sat Feb 25 13:28:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/02_2023/6tg9_10495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/02_2023/6tg9_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_10495/02_2023/6tg9_10495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/02_2023/6tg9_10495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/02_2023/6tg9_10495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tg9_10495/02_2023/6tg9_10495_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 14.48, per 1000 atoms: 0.57 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: 10.92 Conformation dependent library (CDL) restraints added in 4.9 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: 3.41 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: 8.80 Time building geometry restraints manager: 11.35 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: 15011 34.50 - 69.00: 305 69.00 - 103.50: 26 103.50 - 137.99: 2 137.99 - 172.49: 2 Dihedral angle restraints: 15346 sinusoidal: 5952 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 15343 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 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. 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: 0.650 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: 4.450 Check model and map are aligned: 0.390 Process input model: 70.710 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 14.649 172.492 9338 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 % 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 *********************** 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 : 2.873 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 outliers start: 16 outliers final: 2 residues processed: 589 average time/residue: 0.4694 time to fit residues: 402.5393 Evaluate side-chains 362 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2205 time to fit residues: 4.7390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 155 optimal weight: 6.9990 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 ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 26024 Z= 0.203 Angle : 0.626 9.790 35520 Z= 0.307 Chirality : 0.043 0.196 3968 Planarity : 0.005 0.046 4610 Dihedral : 8.272 176.257 3694 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer Outliers : 1.56 % 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: -2.57 (0.25), residues: 340 loop : -2.30 (0.14), residues: 1702 *********************** 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 463 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 423 time to evaluate : 3.115 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 outliers start: 40 outliers final: 26 residues processed: 451 average time/residue: 0.4310 time to fit residues: 297.0259 Evaluate side-chains 374 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 348 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2595 time to fit residues: 16.2797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 296 optimal weight: 30.0000 chunk 320 optimal weight: 0.7980 chunk 264 optimal weight: 0.1980 chunk 294 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** 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: 0.7949 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 26024 Z= 0.285 Angle : 0.626 7.585 35520 Z= 0.309 Chirality : 0.044 0.178 3968 Planarity : 0.005 0.052 4610 Dihedral : 7.863 171.766 3694 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Rotamer Outliers : 2.03 % 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: -1.92 (0.14), residues: 3302 helix: -0.19 (0.15), residues: 1268 sheet: -1.95 (0.25), residues: 386 loop : -1.98 (0.14), residues: 1648 *********************** 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 420 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 368 time to evaluate : 2.888 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 outliers start: 52 outliers final: 26 residues processed: 409 average time/residue: 0.4257 time to fit residues: 268.8643 Evaluate side-chains 360 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 334 time to evaluate : 3.249 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2483 time to fit residues: 16.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 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 96 HIS E 133 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 26024 Z= 0.368 Angle : 0.664 10.341 35520 Z= 0.326 Chirality : 0.046 0.227 3968 Planarity : 0.005 0.056 4610 Dihedral : 7.835 169.165 3694 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.39 % Favored : 94.49 % Rotamer Outliers : 1.95 % 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: -1.67 (0.14), residues: 3302 helix: -0.11 (0.15), residues: 1260 sheet: -1.69 (0.27), residues: 366 loop : -1.76 (0.14), residues: 1676 *********************** 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 410 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 360 time to evaluate : 2.919 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 outliers start: 50 outliers final: 27 residues processed: 398 average time/residue: 0.4258 time to fit residues: 257.0262 Evaluate side-chains 357 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 330 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2477 time to fit residues: 16.4419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS A 941 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 941 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 26024 Z= 0.487 Angle : 0.725 11.572 35520 Z= 0.359 Chirality : 0.049 0.244 3968 Planarity : 0.006 0.072 4610 Dihedral : 7.933 168.467 3694 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.03 % Favored : 93.79 % Rotamer Outliers : 1.99 % 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: -1.72 (0.14), residues: 3302 helix: -0.29 (0.14), residues: 1262 sheet: -1.53 (0.28), residues: 366 loop : -1.71 (0.14), residues: 1674 *********************** 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 388 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 337 time to evaluate : 3.022 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 outliers start: 51 outliers final: 37 residues processed: 377 average time/residue: 0.4376 time to fit residues: 251.6979 Evaluate side-chains 360 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 323 time to evaluate : 2.894 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2882 time to fit residues: 22.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 185 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 315 optimal weight: 0.0370 chunk 261 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 930 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN E 930 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26024 Z= 0.175 Angle : 0.568 7.525 35520 Z= 0.277 Chirality : 0.042 0.148 3968 Planarity : 0.004 0.056 4610 Dihedral : 7.502 170.927 3694 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3302 helix: 0.15 (0.15), residues: 1268 sheet: -1.34 (0.28), residues: 362 loop : -1.50 (0.15), residues: 1672 *********************** 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 388 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 357 time to evaluate : 3.034 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 outliers start: 31 outliers final: 13 residues processed: 378 average time/residue: 0.4117 time to fit residues: 240.1481 Evaluate side-chains 329 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 316 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2377 time to fit residues: 9.6287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 26024 Z= 0.370 Angle : 0.657 10.265 35520 Z= 0.323 Chirality : 0.046 0.212 3968 Planarity : 0.005 0.062 4610 Dihedral : 7.631 172.531 3694 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.81 % Favored : 94.00 % Rotamer Outliers : 1.13 % 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: -1.30 (0.14), residues: 3302 helix: 0.12 (0.15), residues: 1254 sheet: -1.32 (0.28), residues: 366 loop : -1.50 (0.15), residues: 1682 *********************** 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 353 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 3.083 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 outliers start: 29 outliers final: 13 residues processed: 347 average time/residue: 0.4461 time to fit residues: 235.0613 Evaluate side-chains 323 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 310 time to evaluate : 3.231 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2558 time to fit residues: 10.4482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** B 293 ASN B 307 HIS ** 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** F 293 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 26024 Z= 0.464 Angle : 0.716 11.809 35520 Z= 0.355 Chirality : 0.049 0.230 3968 Planarity : 0.005 0.072 4610 Dihedral : 7.825 174.083 3694 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer Outliers : 0.82 % 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: -1.47 (0.14), residues: 3302 helix: -0.13 (0.15), residues: 1266 sheet: -1.39 (0.28), residues: 362 loop : -1.53 (0.15), residues: 1674 *********************** 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 341 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 2.927 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 outliers start: 21 outliers final: 11 residues processed: 328 average time/residue: 0.4513 time to fit residues: 225.3272 Evaluate side-chains 317 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 306 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2500 time to fit residues: 8.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 0.6980 chunk 301 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 292 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 264 optimal weight: 0.0470 chunk 276 optimal weight: 0.7980 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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** B 307 HIS ** 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** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26024 Z= 0.183 Angle : 0.579 8.341 35520 Z= 0.285 Chirality : 0.042 0.140 3968 Planarity : 0.004 0.057 4610 Dihedral : 7.423 173.813 3694 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3302 helix: 0.15 (0.15), residues: 1286 sheet: -1.31 (0.27), residues: 362 loop : -1.38 (0.15), residues: 1654 *********************** 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 333 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 326 time to evaluate : 2.809 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 outliers start: 7 outliers final: 5 residues processed: 330 average time/residue: 0.4435 time to fit residues: 224.5256 Evaluate side-chains 318 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 2.925 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2390 time to fit residues: 6.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 258 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.069 26024 Z= 0.521 Angle : 0.734 12.406 35520 Z= 0.365 Chirality : 0.051 0.215 3968 Planarity : 0.006 0.080 4610 Dihedral : 7.767 173.772 3694 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer Outliers : 0.39 % 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: -1.41 (0.14), residues: 3302 helix: -0.10 (0.15), residues: 1270 sheet: -1.42 (0.27), residues: 362 loop : -1.46 (0.15), residues: 1670 ********************** 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 317 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 307 time to evaluate : 2.921 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 outliers start: 10 outliers final: 6 residues processed: 313 average time/residue: 0.4640 time to fit residues: 219.4624 Evaluate side-chains 307 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 301 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2589 time to fit residues: 6.7833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 275 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 238 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** 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** ** 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 = 0.3841 r_free = 0.3841 target = 0.157181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125670 restraints weight = 32430.325| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.88 r_work: 0.3194 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4296 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= 0.234 Angle : 0.608 7.784 35520 Z= 0.299 Chirality : 0.043 0.154 3968 Planarity : 0.005 0.056 4610 Dihedral : 7.506 175.059 3694 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer Outliers : 0.20 % 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: -1.22 (0.14), residues: 3302 helix: 0.06 (0.15), residues: 1276 sheet: -1.39 (0.27), residues: 358 loop : -1.33 (0.15), residues: 1668 =============================================================================== Job complete usr+sys time: 5477.75 seconds wall clock time: 101 minutes 24.99 seconds (6084.99 seconds total)