Starting phenix.real_space_refine on Sat Dec 16 13:33:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4l_12722/12_2023/7o4l_12722_updated.pdb" } resolution = 3.4 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= 0.052 sd= 1.010 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 11 6.06 5 P 22 5.49 5 Mg 1 5.21 5 S 210 5.16 5 Be 1 3.05 5 C 22270 2.51 5 N 6004 2.21 5 O 6633 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 67": "NH1" <-> "NH2" Residue "0 ARG 104": "NH1" <-> "NH2" Residue "0 GLU 131": "OE1" <-> "OE2" Residue "0 GLU 186": "OE1" <-> "OE2" Residue "0 ARG 197": "NH1" <-> "NH2" Residue "0 GLU 225": "OE1" <-> "OE2" Residue "0 ARG 270": "NH1" <-> "NH2" Residue "0 GLU 273": "OE1" <-> "OE2" Residue "0 TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 287": "OE1" <-> "OE2" Residue "0 GLU 304": "OE1" <-> "OE2" Residue "0 GLU 319": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 ARG 380": "NH1" <-> "NH2" Residue "0 GLU 424": "OE1" <-> "OE2" Residue "0 TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 509": "NH1" <-> "NH2" Residue "0 ARG 520": "NH1" <-> "NH2" Residue "0 GLU 528": "OE1" <-> "OE2" Residue "0 TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 572": "OE1" <-> "OE2" Residue "0 TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 594": "NH1" <-> "NH2" Residue "0 GLU 608": "OE1" <-> "OE2" Residue "0 GLU 631": "OE1" <-> "OE2" Residue "0 ARG 638": "NH1" <-> "NH2" Residue "0 GLU 640": "OE1" <-> "OE2" Residue "0 ARG 671": "NH1" <-> "NH2" Residue "0 ARG 685": "NH1" <-> "NH2" Residue "0 ARG 688": "NH1" <-> "NH2" Residue "0 ARG 690": "NH1" <-> "NH2" Residue "0 ARG 722": "NH1" <-> "NH2" Residue "0 ARG 751": "NH1" <-> "NH2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 86": "NH1" <-> "NH2" Residue "1 ARG 110": "NH1" <-> "NH2" Residue "1 ARG 121": "NH1" <-> "NH2" Residue "1 ARG 253": "NH1" <-> "NH2" Residue "1 GLU 261": "OE1" <-> "OE2" Residue "1 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "1 ARG 416": "NH1" <-> "NH2" Residue "1 ARG 502": "NH1" <-> "NH2" Residue "1 GLU 537": "OE1" <-> "OE2" Residue "1 GLU 548": "OE1" <-> "OE2" Residue "1 ARG 551": "NH1" <-> "NH2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 GLU 54": "OE1" <-> "OE2" Residue "2 GLU 126": "OE1" <-> "OE2" Residue "2 GLU 187": "OE1" <-> "OE2" Residue "2 ARG 247": "NH1" <-> "NH2" Residue "2 ARG 254": "NH1" <-> "NH2" Residue "2 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 342": "OE1" <-> "OE2" Residue "2 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ARG 380": "NH1" <-> "NH2" Residue "2 ARG 384": "NH1" <-> "NH2" Residue "2 ARG 385": "NH1" <-> "NH2" Residue "2 GLU 401": "OE1" <-> "OE2" Residue "2 GLU 428": "OE1" <-> "OE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 467": "OE1" <-> "OE2" Residue "3 GLU 40": "OE1" <-> "OE2" Residue "3 GLU 130": "OE1" <-> "OE2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 ARG 146": "NH1" <-> "NH2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 GLU 166": "OE1" <-> "OE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 GLU 239": "OE1" <-> "OE2" Residue "4 ARG 281": "NH1" <-> "NH2" Residue "4 GLU 314": "OE1" <-> "OE2" Residue "6 ARG 142": "NH1" <-> "NH2" Residue "6 GLU 285": "OE1" <-> "OE2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 ARG 327": "NH1" <-> "NH2" Residue "6 GLU 330": "OE1" <-> "OE2" Residue "6 ARG 409": "NH1" <-> "NH2" Residue "6 ARG 426": "NH1" <-> "NH2" Residue "6 ARG 428": "NH1" <-> "NH2" Residue "7 ARG 114": "NH1" <-> "NH2" Residue "7 ARG 122": "NH1" <-> "NH2" Residue "7 ARG 124": "NH1" <-> "NH2" Residue "7 ARG 140": "NH1" <-> "NH2" Residue "7 GLU 189": "OE1" <-> "OE2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 GLU 324": "OE1" <-> "OE2" Residue "7 ARG 329": "NH1" <-> "NH2" Residue "7 ARG 344": "NH1" <-> "NH2" Residue "7 ARG 378": "NH1" <-> "NH2" Residue "7 ARG 421": "NH1" <-> "NH2" Residue "7 GLU 444": "OE1" <-> "OE2" Residue "7 GLU 449": "OE1" <-> "OE2" Residue "7 ARG 480": "NH1" <-> "NH2" Residue "7 GLU 481": "OE1" <-> "OE2" Residue "7 ARG 519": "NH1" <-> "NH2" Residue "7 GLU 537": "OE1" <-> "OE2" Residue "7 ARG 571": "NH1" <-> "NH2" Residue "7 GLU 572": "OE1" <-> "OE2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 686": "NH1" <-> "NH2" Residue "7 ARG 692": "NH1" <-> "NH2" Residue "7 ARG 696": "NH1" <-> "NH2" Residue "7 TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 762": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W GLU 40": "OE1" <-> "OE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W GLU 196": "OE1" <-> "OE2" Residue "W GLU 200": "OE1" <-> "OE2" Residue "W ARG 205": "NH1" <-> "NH2" Residue "W ARG 274": "NH1" <-> "NH2" Residue "W ARG 279": "NH1" <-> "NH2" Residue "W GLU 283": "OE1" <-> "OE2" Residue "W ARG 285": "NH1" <-> "NH2" Residue "W GLU 292": "OE1" <-> "OE2" Residue "W ARG 351": "NH1" <-> "NH2" Residue "W GLU 352": "OE1" <-> "OE2" Residue "W GLU 410": "OE1" <-> "OE2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 234": "NH1" <-> "NH2" Residue "X ARG 276": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35159 Number of models: 1 Model: "" Number of chains: 25 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4206 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2946 Classifications: {'peptide': 374} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 352} Chain breaks: 2 Chain: "7" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4881 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 23, 'TRANS': 583} Chain breaks: 1 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1752 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 15, 'TRANS': 211} Chain breaks: 13 Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 644 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "D" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1296 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Chain: "F" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 454 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain breaks: 3 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2521 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 3 Chain: "X" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1094 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 53.305 87.610 111.138 1.00 63.26 S ATOM 1265 SG CYS 0 156 48.122 87.031 115.179 1.00 77.00 S ATOM 1080 SG CYS 0 133 50.264 92.885 113.038 1.00 69.84 S ATOM 1566 SG CYS 0 191 53.156 89.858 117.401 1.00 64.35 S ATOM 13933 SG CYS 3 13 37.976 118.384 65.689 1.00104.51 S ATOM 13954 SG CYS 3 16 39.251 118.003 62.130 1.00101.65 S ATOM 14149 SG CYS 3 39 40.467 120.890 64.340 1.00103.25 S ATOM 14170 SG CYS 3 42 36.954 120.939 63.040 1.00105.49 S ATOM 14102 SG CYS 3 34 30.720 122.926 75.103 1.00109.81 S ATOM 14260 SG CYS 3 54 30.221 122.083 71.321 1.00113.01 S ATOM 14298 SG CYS 3 59 27.223 121.640 73.766 1.00112.15 S ATOM 16962 SG CYS 4 289 103.510 47.782 132.190 1.00 69.24 S ATOM 16981 SG CYS 4 292 106.054 49.896 133.735 1.00 69.60 S ATOM 17073 SG CYS 4 305 103.947 47.292 135.863 1.00 83.87 S ATOM 17091 SG CYS 4 308 102.428 50.451 134.880 1.00 80.35 S ATOM 19910 SG CYS 6 349 106.712 31.471 118.303 1.00 70.67 S ATOM 19931 SG CYS 6 352 104.837 29.075 115.914 1.00 84.21 S ATOM 20010 SG CYS 6 363 105.159 32.686 115.060 1.00 70.40 S ATOM 20029 SG CYS 6 366 103.050 31.818 118.074 1.00 79.85 S ATOM 20331 SG CYS 6 403 133.275 66.879 130.651 1.00 79.50 S ATOM 20354 SG CYS 6 406 135.029 65.673 127.494 1.00 65.11 S ATOM 20548 SG CYS 6 437 132.463 68.433 127.253 1.00 76.82 S ATOM 20569 SG CYS 6 440 131.314 64.916 128.060 1.00 68.36 S ATOM 20481 SG CYS 6 429 123.018 64.588 136.919 1.00 87.01 S ATOM 20504 SG CYS 6 432 126.218 63.322 138.560 1.00 82.85 S ATOM 20662 SG CYS 6 451 125.519 62.371 135.001 1.00 65.89 S ATOM 20679 SG CYS 6 454 123.280 60.950 137.738 1.00 71.51 S ATOM 19809 SG CYS 6 336 110.717 32.383 104.613 1.00 94.03 S ATOM 19821 SG CYS 6 338 109.539 35.166 107.006 1.00 85.00 S ATOM 19969 SG CYS 6 357 113.247 34.670 106.257 1.00 76.59 S ATOM 26068 SG CYS A 107 77.693 113.377 39.038 1.00 94.87 S ATOM 26092 SG CYS A 110 76.676 114.657 42.418 1.00 88.57 S ATOM 26173 SG CYS A 148 80.347 113.702 41.735 1.00 93.73 S ATOM 26214 SG CYS A 167 77.646 110.995 41.943 1.00 95.42 S ATOM 25856 SG CYS A 67 39.135 138.222 24.376 1.00 62.24 S ATOM 25878 SG CYS A 70 39.568 141.735 25.846 1.00 55.94 S ATOM 25911 SG CYS A 77 41.887 140.546 23.035 1.00 65.22 S ATOM 27520 SG CYS B1163 51.902 142.987 36.674 1.00 51.22 S ATOM 27538 SG CYS B1166 53.454 140.073 34.647 1.00 50.73 S ATOM 27663 SG CYS B1182 49.734 140.166 35.405 1.00 41.66 S ATOM 27682 SG CYS B1185 52.317 139.483 38.143 1.00 43.23 S ATOM 32503 SG CYS W 124 25.224 134.963 33.154 1.00 87.67 S ATOM 32524 SG CYS W 127 28.579 134.255 31.645 1.00 88.86 S ATOM 32709 SG CYS W 149 27.645 137.830 32.704 1.00 77.79 S ATOM 32729 SG CYS W 152 26.054 136.210 29.624 1.00 80.54 S Time building chain proxies: 19.14, per 1000 atoms: 0.54 Number of scatterers: 35159 At special positions: 0 Unit cell: (193.2, 198.45, 166.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 11 29.99 Fe 4 26.01 S 210 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 6633 8.00 N 6004 7.00 C 22270 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.80 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 57 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 29 sheets defined 44.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.46 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.857A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 169 No H-bonds generated for 'chain '0' and resid 167 through 169' Processing helix chain '0' and resid 178 through 188 Processing helix chain '0' and resid 192 through 198 Processing helix chain '0' and resid 210 through 212 No H-bonds generated for 'chain '0' and resid 210 through 212' Processing helix chain '0' and resid 216 through 218 No H-bonds generated for 'chain '0' and resid 216 through 218' Processing helix chain '0' and resid 220 through 223 No H-bonds generated for 'chain '0' and resid 220 through 223' Processing helix chain '0' and resid 237 through 247 removed outlier: 5.423A pdb=" N ASP 0 241 " --> pdb=" O HIS 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 Processing helix chain '0' and resid 280 through 291 removed outlier: 3.637A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 347 removed outlier: 3.993A pdb=" N LYS 0 347 " --> pdb=" O LYS 0 343 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.587A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 396 through 411 removed outlier: 3.613A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 444 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 466 through 472 Proline residue: 0 470 - end of helix No H-bonds generated for 'chain '0' and resid 466 through 472' Processing helix chain '0' and resid 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.709A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 592 Processing helix chain '0' and resid 633 through 646 Processing helix chain '0' and resid 650 through 668 removed outlier: 3.602A pdb=" N CYS 0 665 " --> pdb=" O HIS 0 661 " (cutoff:3.500A) Processing helix chain '0' and resid 685 through 692 removed outlier: 3.718A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 removed outlier: 3.659A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 704 through 706 No H-bonds generated for 'chain '0' and resid 704 through 706' Processing helix chain '0' and resid 710 through 724 Processing helix chain '0' and resid 730 through 733 No H-bonds generated for 'chain '0' and resid 730 through 733' Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 94 through 120 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 190 through 199 Processing helix chain '1' and resid 206 through 223 removed outlier: 3.744A pdb=" N TRP 1 210 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE 1 214 " --> pdb=" O TRP 1 210 " (cutoff:3.500A) Proline residue: 1 215 - end of helix Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 273 removed outlier: 3.654A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN 1 273 " --> pdb=" O ALA 1 269 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 288 removed outlier: 3.626A pdb=" N TRP 1 284 " --> pdb=" O GLU 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.836A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 340 through 344 Processing helix chain '1' and resid 356 through 358 No H-bonds generated for 'chain '1' and resid 356 through 358' Processing helix chain '1' and resid 371 through 389 Processing helix chain '1' and resid 414 through 419 removed outlier: 3.707A pdb=" N GLU 1 418 " --> pdb=" O ASP 1 414 " (cutoff:3.500A) Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 493 through 516 removed outlier: 3.528A pdb=" N GLN 1 513 " --> pdb=" O ILE 1 509 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 570 Processing helix chain '1' and resid 573 through 603 removed outlier: 3.573A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 638 Proline residue: 1 618 - end of helix Processing helix chain '2' and resid 6 through 16 removed outlier: 4.235A pdb=" N THR 2 11 " --> pdb=" O LYS 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 27 removed outlier: 3.935A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 69 through 83 removed outlier: 4.584A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN 2 73 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 196 through 210 Processing helix chain '2' and resid 218 through 230 removed outlier: 3.672A pdb=" N ALA 2 230 " --> pdb=" O PHE 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 Processing helix chain '2' and resid 273 through 279 Processing helix chain '2' and resid 354 through 362 Processing helix chain '2' and resid 380 through 389 Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 422 Processing helix chain '2' and resid 435 through 450 removed outlier: 3.636A pdb=" N LEU 2 448 " --> pdb=" O TRP 2 444 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP 2 449 " --> pdb=" O GLN 2 445 " (cutoff:3.500A) Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 47 Processing helix chain '3' and resid 76 through 91 Processing helix chain '3' and resid 97 through 99 No H-bonds generated for 'chain '3' and resid 97 through 99' Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 Processing helix chain '4' and resid 34 through 43 Processing helix chain '4' and resid 50 through 67 Processing helix chain '4' and resid 116 through 140 removed outlier: 3.858A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 205 removed outlier: 4.342A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 223 through 229 Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 258 No H-bonds generated for 'chain '4' and resid 256 through 258' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 321 Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 61 removed outlier: 4.468A pdb=" N GLU 5 48 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL 5 50 " --> pdb=" O VAL 5 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 5 54 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU 5 58 " --> pdb=" O ASN 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 78 No H-bonds generated for 'chain '6' and resid 75 through 78' Processing helix chain '6' and resid 83 through 86 No H-bonds generated for 'chain '6' and resid 83 through 86' Processing helix chain '6' and resid 97 through 113 removed outlier: 3.797A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 200 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 257 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 305 removed outlier: 3.972A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 383 removed outlier: 4.137A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU 6 383 " --> pdb=" O SER 6 379 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 removed outlier: 3.505A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 108 through 112 removed outlier: 4.431A pdb=" N GLY 7 111 " --> pdb=" O SER 7 108 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 160 Processing helix chain '7' and resid 177 through 185 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 217 removed outlier: 3.970A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 240 through 247 removed outlier: 3.554A pdb=" N MET 7 244 " --> pdb=" O ASP 7 240 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 332 removed outlier: 4.198A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 373 removed outlier: 3.686A pdb=" N MET 7 373 " --> pdb=" O SER 7 369 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 426 Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 468 through 479 removed outlier: 3.588A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 504 removed outlier: 3.631A pdb=" N THR 7 504 " --> pdb=" O VAL 7 501 " (cutoff:3.500A) Processing helix chain '7' and resid 524 through 530 Processing helix chain '7' and resid 540 through 546 Processing helix chain '7' and resid 563 through 571 removed outlier: 3.799A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.660A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR 7 581 " --> pdb=" O ARG 7 577 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 659 Processing helix chain '7' and resid 680 through 690 removed outlier: 4.379A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) Processing helix chain '7' and resid 694 through 696 No H-bonds generated for 'chain '7' and resid 694 through 696' Processing helix chain '7' and resid 714 through 729 removed outlier: 4.051A pdb=" N ALA 7 724 " --> pdb=" O THR 7 720 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 removed outlier: 3.583A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 286 through 303 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 1396 through 1399 No H-bonds generated for 'chain 'A' and resid 1396 through 1399' Processing helix chain 'A' and resid 1410 through 1414 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.780A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.062A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 116 Processing helix chain 'W' and resid 133 through 138 removed outlier: 3.877A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 178 removed outlier: 4.245A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS W 168 " --> pdb=" O ASN W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 191 Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.853A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 287 Processing helix chain 'W' and resid 292 through 294 No H-bonds generated for 'chain 'W' and resid 292 through 294' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 189 through 198 Processing helix chain 'X' and resid 207 through 211 Processing helix chain 'X' and resid 218 through 227 Processing helix chain 'X' and resid 257 through 265 Processing helix chain 'X' and resid 274 through 281 Processing helix chain 'X' and resid 290 through 292 No H-bonds generated for 'chain 'X' and resid 290 through 292' Processing sheet with id= A, first strand: chain '0' and resid 2 through 5 Processing sheet with id= B, first strand: chain '0' and resid 105 through 107 removed outlier: 6.641A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER 0 38 " --> pdb=" O ILE 0 458 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 495 through 497 removed outlier: 6.677A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 259 through 261 Processing sheet with id= I, first strand: chain '2' and resid 339 through 341 removed outlier: 6.339A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 456 through 459 removed outlier: 6.184A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 28 through 30 Processing sheet with id= L, first strand: chain '4' and resid 82 through 87 removed outlier: 6.352A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL 4 178 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP 4 211 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR 4 180 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL 4 213 " --> pdb=" O THR 4 180 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 8 through 11 Processing sheet with id= N, first strand: chain '6' and resid 178 through 183 removed outlier: 6.651A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 326 through 328 removed outlier: 3.749A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 132 through 134 removed outlier: 6.358A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 435 through 438 removed outlier: 6.465A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE 7 438 " --> pdb=" O LEU 7 452 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL 7 454 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL 7 385 " --> pdb=" O LEU 7 535 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU 7 537 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 703 through 710 removed outlier: 3.806A pdb=" N PHE 7 705 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS 7 734 " --> pdb=" O GLU 7 556 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP 7 558 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE 7 736 " --> pdb=" O TRP 7 558 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 651 through 653 removed outlier: 6.481A pdb=" N ILE 7 605 " --> pdb=" O ILE 7 652 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS 7 669 " --> pdb=" O ILE 7 606 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE 7 608 " --> pdb=" O CYS 7 669 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 7 671 " --> pdb=" O PHE 7 608 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= U, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= V, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= W, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= X, first strand: chain 'F' and resid 133 through 136 Processing sheet with id= Y, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.263A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.708A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS G 158 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AB, first strand: chain 'W' and resid 37 through 39 Processing sheet with id= AC, first strand: chain 'X' and resid 230 through 232 1365 hydrogen bonds defined for protein. 3690 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: 12.05 Time building geometry restraints manager: 15.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 14227 1.41 - 1.63: 21261 1.63 - 1.85: 317 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 35817 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C TYR 0 616 " pdb=" O TYR 0 616 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.20e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 35812 not shown) Histogram of bond angle deviations from ideal: 73.67 - 85.73: 12 85.73 - 97.80: 0 97.80 - 109.86: 4083 109.86 - 121.93: 37283 121.93 - 133.99: 7027 Bond angle restraints: 48405 Sorted by residual: angle pdb=" N PHE 7 565 " pdb=" CA PHE 7 565 " pdb=" C PHE 7 565 " ideal model delta sigma weight residual 111.28 117.10 -5.82 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N ASP 0 613 " pdb=" CA ASP 0 613 " pdb=" C ASP 0 613 " ideal model delta sigma weight residual 110.46 116.89 -6.43 1.48e+00 4.57e-01 1.89e+01 angle pdb=" CA PHE 7 565 " pdb=" CB PHE 7 565 " pdb=" CG PHE 7 565 " ideal model delta sigma weight residual 113.80 117.74 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA HIS 0 614 " pdb=" C HIS 0 614 " pdb=" O HIS 0 614 " ideal model delta sigma weight residual 120.51 114.92 5.59 1.43e+00 4.89e-01 1.53e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 99.40 11.60 3.00e+00 1.11e-01 1.50e+01 ... (remaining 48400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 20742 23.68 - 47.36: 1071 47.36 - 71.03: 117 71.03 - 94.71: 44 94.71 - 118.39: 2 Dihedral angle restraints: 21976 sinusoidal: 9272 harmonic: 12704 Sorted by residual: dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 58.39 -118.39 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -175.26 115.27 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 1.79 -61.80 1 2.00e+01 2.50e-03 1.27e+01 ... (remaining 21973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5087 0.076 - 0.153: 412 0.153 - 0.229: 2 0.229 - 0.305: 0 0.305 - 0.381: 2 Chirality restraints: 5503 Sorted by residual: chirality pdb=" CA PHE 7 565 " pdb=" N PHE 7 565 " pdb=" C PHE 7 565 " pdb=" CB PHE 7 565 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE 6 301 " pdb=" N PHE 6 301 " pdb=" C PHE 6 301 " pdb=" CB PHE 6 301 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 5500 not shown) Planarity restraints: 6101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 0 613 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASP 0 613 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP 0 613 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS 0 614 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 7 565 " -0.008 2.00e-02 2.50e+03 1.65e-02 4.76e+00 pdb=" CG PHE 7 565 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE 7 565 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE 7 565 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE 7 565 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE 7 565 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE 7 565 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO 5 14 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 6098 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 265 2.58 - 3.16: 29810 3.16 - 3.74: 53073 3.74 - 4.32: 73341 4.32 - 4.90: 122773 Nonbonded interactions: 279262 Sorted by model distance: nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.120 nonbonded pdb="MG MG 7 902 " pdb=" O1B ADP 7 903 " model vdw 2.001 2.170 nonbonded pdb=" O PHE 0 529 " pdb=" OG1 THR 0 533 " model vdw 2.025 2.440 nonbonded pdb=" OD1 ASN 5 43 " pdb=" OG SER 5 45 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR 3 35 " pdb=" OD2 ASP 3 83 " model vdw 2.073 2.440 ... (remaining 279257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.060 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 108.470 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.002 0.109 35817 Z= 0.146 Angle : 0.451 11.600 48405 Z= 0.256 Chirality : 0.038 0.381 5503 Planarity : 0.002 0.047 6101 Dihedral : 14.103 118.391 13696 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 2.39 (0.14), residues: 4226 helix: 3.11 (0.12), residues: 1947 sheet: 0.42 (0.24), residues: 513 loop : 0.23 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 201 HIS 0.002 0.000 HIS W 93 PHE 0.034 0.001 PHE 7 565 TYR 0.015 0.001 TYR 7 581 ARG 0.003 0.000 ARG 7 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 901 time to evaluate : 4.294 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: 0 outliers final: 0 residues processed: 901 average time/residue: 0.5025 time to fit residues: 718.8553 Evaluate side-chains 660 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 3.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 0.9990 chunk 325 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 337 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 250 optimal weight: 0.4980 chunk 390 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 239 ASN 0 291 GLN 0 707 ASN ** 1 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 245 ASN 1 262 ASN 1 510 ASN 1 513 GLN 1 628 HIS 2 12 GLN 2 261 GLN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 226 GLN 6 445 HIS 6 450 ASN 7 154 GLN 7 644 GLN A 169 ASN A 493 GLN D 31 GLN D 132 GLN G 57 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35817 Z= 0.251 Angle : 0.547 8.796 48405 Z= 0.282 Chirality : 0.041 0.175 5503 Planarity : 0.004 0.045 6101 Dihedral : 7.736 110.036 4888 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.48 % Allowed : 9.29 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.71 (0.13), residues: 4226 helix: 2.33 (0.12), residues: 1963 sheet: 0.28 (0.24), residues: 497 loop : 0.09 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 201 HIS 0.006 0.001 HIS 1 628 PHE 0.023 0.002 PHE 1 9 TYR 0.026 0.001 TYR 7 341 ARG 0.010 0.000 ARG 7 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 683 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 40 residues processed: 707 average time/residue: 0.4905 time to fit residues: 559.0378 Evaluate side-chains 669 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 629 time to evaluate : 4.481 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3446 time to fit residues: 31.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 391 optimal weight: 1.9990 chunk 422 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 387 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 291 GLN 1 510 ASN ** 2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 389 ASN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 62 ASN 4 226 GLN 6 450 ASN 7 127 HIS 7 548 HIS 7 642 ASN 7 644 GLN A 213 HIS D 157 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 35817 Z= 0.545 Angle : 0.644 11.604 48405 Z= 0.333 Chirality : 0.046 0.206 5503 Planarity : 0.005 0.057 6101 Dihedral : 8.161 112.685 4888 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.46 % Allowed : 12.82 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.05 (0.13), residues: 4226 helix: 1.68 (0.12), residues: 1970 sheet: -0.08 (0.23), residues: 488 loop : -0.11 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 4 37 HIS 0.009 0.001 HIS 0 211 PHE 0.042 0.002 PHE A 22 TYR 0.027 0.002 TYR 7 628 ARG 0.008 0.001 ARG 7 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 674 time to evaluate : 4.009 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: 57 outliers final: 36 residues processed: 700 average time/residue: 0.4984 time to fit residues: 562.6462 Evaluate side-chains 663 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 627 time to evaluate : 4.231 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3293 time to fit residues: 28.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 0.1980 chunk 294 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 415 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 372 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 427 ASN 1 3 HIS 1 245 ASN 1 628 HIS 2 20 GLN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 ASN 4 226 GLN 5 61 ASN 7 644 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN B1195 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 35817 Z= 0.210 Angle : 0.525 8.913 48405 Z= 0.269 Chirality : 0.040 0.194 5503 Planarity : 0.004 0.052 6101 Dihedral : 8.024 116.986 4888 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.07 % Allowed : 14.18 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.10 (0.13), residues: 4226 helix: 1.77 (0.12), residues: 1960 sheet: -0.16 (0.23), residues: 509 loop : -0.11 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 7 482 HIS 0.008 0.001 HIS 7 738 PHE 0.019 0.001 PHE 1 634 TYR 0.022 0.001 TYR 4 79 ARG 0.006 0.000 ARG 6 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 664 time to evaluate : 4.003 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: 42 outliers final: 26 residues processed: 680 average time/residue: 0.4936 time to fit residues: 542.4325 Evaluate side-chains 647 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 621 time to evaluate : 4.007 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3212 time to fit residues: 21.6135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 354 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 373 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 291 GLN 2 110 ASN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 226 GLN 7 127 HIS 7 471 GLN 7 644 GLN ** 7 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 35817 Z= 0.270 Angle : 0.536 9.937 48405 Z= 0.273 Chirality : 0.041 0.172 5503 Planarity : 0.004 0.052 6101 Dihedral : 8.010 119.979 4888 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.02 % Allowed : 15.35 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.03 (0.13), residues: 4226 helix: 1.69 (0.12), residues: 1970 sheet: -0.12 (0.23), residues: 502 loop : -0.16 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 65 HIS 0.010 0.001 HIS 7 127 PHE 0.020 0.001 PHE 1 634 TYR 0.040 0.001 TYR 2 270 ARG 0.006 0.000 ARG 0 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 635 time to evaluate : 4.256 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: 40 outliers final: 23 residues processed: 662 average time/residue: 0.4386 time to fit residues: 469.9033 Evaluate side-chains 638 residues out of total 3908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 615 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2961 time to fit residues: 17.0301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 6.9990 chunk 374 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 416 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 218 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: