Starting phenix.real_space_refine on Sat Sep 28 14:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/09_2024/6pb5_20287_trim.cif" } resolution = 4.52 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= -0.020 sd= 0.262 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 158 5.49 5 Mg 1 5.21 5 S 147 5.16 5 C 21701 2.51 5 N 6264 2.21 5 O 7104 1.98 5 H 34319 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69696 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 21054 Classifications: {'peptide': 1334} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1276} Chain breaks: 1 Chain: "D" Number of atoms: 21012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21012 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 7892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 7892 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 15, 'TRANS': 466} Chain breaks: 1 Chain: "G" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3154 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "H" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3155 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "1" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2480 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "2" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2486 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29109 SG CYS D 70 122.914 125.710 67.439 1.00 20.00 S ATOM 29138 SG CYS D 72 124.561 126.693 70.401 1.00 20.00 S ATOM 29416 SG CYS D 88 125.925 122.311 69.136 1.00 20.00 S ATOM 40950 SG CYS D 814 90.491 80.871 20.327 1.00 20.00 S ATOM 42088 SG CYS D 888 91.542 81.732 23.612 1.00 20.00 S ATOM 42179 SG CYS D 895 88.248 82.581 22.524 1.00 20.00 S ATOM 42216 SG CYS D 898 87.814 79.356 23.550 1.00 20.00 S Time building chain proxies: 23.31, per 1000 atoms: 0.33 Number of scatterers: 69696 At special positions: 0 Unit cell: (201.6, 204.3, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 158 15.00 Mg 1 11.99 O 7104 8.00 N 6264 7.00 C 21701 6.00 H 34319 1.00 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 - 3.00 Amino acid : True - 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: 13.93 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 55 sheets defined 42.4% alpha, 11.0% beta 47 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 26.26 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 removed outlier: 3.538A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.025A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.661A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 35 through 51 removed outlier: 4.182A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.727A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.898A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 4.792A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 457 through 482 removed outlier: 4.130A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 496 through 506 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.901A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 4.295A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.879A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.772A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.726A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 860 removed outlier: 3.522A pdb=" N ALA C 860 " --> pdb=" O VAL C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 865 removed outlier: 3.700A pdb=" N LEU C 865 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 876 removed outlier: 3.585A pdb=" N ALA C 875 " --> pdb=" O VAL C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 943 through 970 Processing helix chain 'C' and resid 971 through 981 removed outlier: 3.847A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 removed outlier: 4.008A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.589A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.687A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 Processing helix chain 'C' and resid 1298 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 4.004A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.884A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.110A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 182 through 192 Processing helix chain 'D' and resid 194 through 208 removed outlier: 3.595A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.721A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.881A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.806A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.906A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 455 removed outlier: 3.806A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.061A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.813A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 650 through 671 removed outlier: 3.764A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 700 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 788 removed outlier: 3.531A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 803 removed outlier: 3.649A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 916 through 928 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.500A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.915A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.692A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1288 Processing helix chain 'D' and resid 1309 through 1315 Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 3.602A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.895A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.743A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.789A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.511A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 143 through 153 removed outlier: 4.073A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 236 removed outlier: 3.955A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 255 Processing helix chain 'F' and resid 264 through 293 removed outlier: 3.697A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 310 removed outlier: 4.121A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 308 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 320 removed outlier: 3.734A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 333 through 352 removed outlier: 3.539A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 3.523A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 394 removed outlier: 3.826A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.923A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.776A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 488 removed outlier: 3.708A pdb=" N MET F 487 " --> pdb=" O LEU F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.850A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 4.019A pdb=" N PHE F 522 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 549 Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 599 removed outlier: 3.583A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 609 removed outlier: 4.097A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 18 removed outlier: 3.562A pdb=" N HIS G 17 " --> pdb=" O TRP G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.976A pdb=" N LEU G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 71 through 76' Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'G' and resid 112 through 136 Processing helix chain 'G' and resid 138 through 153 Processing helix chain 'G' and resid 170 through 177 Processing helix chain 'G' and resid 179 through 193 removed outlier: 3.600A pdb=" N VAL G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 16 Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.503A pdb=" N GLY H 74 " --> pdb=" O GLY H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 109 removed outlier: 3.858A pdb=" N GLN H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 137 removed outlier: 3.833A pdb=" N MET H 114 " --> pdb=" O PRO H 110 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 170 through 177 Processing helix chain 'H' and resid 180 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.546A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 182 through 187 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 6.987A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.414A pdb=" N ALA B 190 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 197 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.413A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.517A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 104 through 106 removed outlier: 7.648A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 112 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.597A pdb=" N PHE C 136 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.872A pdb=" N GLN C 148 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 454 " --> pdb=" O GLN C 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 176 removed outlier: 4.339A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.541A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC2, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 303 removed outlier: 7.118A pdb=" N ASP C 303 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 529 through 530 removed outlier: 3.645A pdb=" N ILE C 530 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C 573 " --> pdb=" O ILE C 530 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 598 through 607 removed outlier: 3.746A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 638 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 722 through 727 removed outlier: 6.094A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1075 through 1080 removed outlier: 7.034A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 832 removed outlier: 4.626A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG C1058 " --> pdb=" O THR C 830 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 835 through 840 removed outlier: 3.889A pdb=" N TYR C1053 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AD5, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.610A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 365 through 369 removed outlier: 5.846A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 421 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 547 through 552 Processing sheet with id=AE2, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.548A pdb=" N THR D 810 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'D' and resid 981 through 985 removed outlier: 6.777A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1028 through 1029 Processing sheet with id=AE9, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.608A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1106 through 1107 Processing sheet with id=AF2, first strand: chain 'D' and resid 1175 through 1178 removed outlier: 4.088A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1263 through 1265 Processing sheet with id=AF4, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.559A pdb=" N GLU G 96 " --> pdb=" O HIS G 19 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU G 93 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.961A pdb=" N THR G 28 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA G 88 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE G 30 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.961A pdb=" N THR G 28 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA G 88 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE G 30 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 164 through 165 Processing sheet with id=AF8, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AF9, first strand: chain 'H' and resid 28 through 30 removed outlier: 6.121A pdb=" N VAL H 86 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 157 through 158 1309 hydrogen bonds defined for protein. 3681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 29.48 Time building geometry restraints manager: 17.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 34287 1.01 - 1.21: 43 1.21 - 1.42: 14716 1.42 - 1.62: 21254 1.62 - 1.83: 261 Bond restraints: 70561 Sorted by residual: bond pdb=" C ILE C1079 " pdb=" N ASN C1080 " ideal model delta sigma weight residual 1.333 1.229 0.104 1.61e-02 3.86e+03 4.16e+01 bond pdb=" C ARG B 91 " pdb=" N VAL B 92 " ideal model delta sigma weight residual 1.334 1.277 0.057 1.29e-02 6.01e+03 1.98e+01 bond pdb=" CG LEU C 979 " pdb=" CD2 LEU C 979 " ideal model delta sigma weight residual 1.521 1.383 0.138 3.30e-02 9.18e+02 1.76e+01 bond pdb=" N ASN D 792 " pdb=" CA ASN D 792 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" CG HIS H 31 " pdb=" ND1 HIS H 31 " ideal model delta sigma weight residual 1.378 1.420 -0.042 1.10e-02 8.26e+03 1.45e+01 ... (remaining 70556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 125373 3.39 - 6.79: 2473 6.79 - 10.18: 138 10.18 - 13.57: 18 13.57 - 16.96: 3 Bond angle restraints: 128005 Sorted by residual: angle pdb=" C GLN A 147 " pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 121.54 134.81 -13.27 1.91e+00 2.74e-01 4.83e+01 angle pdb=" N LEU C 246 " pdb=" CA LEU C 246 " pdb=" C LEU C 246 " ideal model delta sigma weight residual 109.71 100.71 9.00 1.41e+00 5.03e-01 4.07e+01 angle pdb=" N LEU D 672 " pdb=" CA LEU D 672 " pdb=" C LEU D 672 " ideal model delta sigma weight residual 110.80 98.52 12.28 2.13e+00 2.20e-01 3.32e+01 angle pdb=" C PRO F 263 " pdb=" N LYS F 264 " pdb=" CA LYS F 264 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" N GLY D1308 " pdb=" CA GLY D1308 " pdb=" C GLY D1308 " ideal model delta sigma weight residual 111.85 117.86 -6.01 1.06e+00 8.90e-01 3.22e+01 ... (remaining 128000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 30519 34.09 - 68.18: 1623 68.18 - 102.27: 34 102.27 - 136.36: 4 136.36 - 170.45: 6 Dihedral angle restraints: 32186 sinusoidal: 19113 harmonic: 13073 Sorted by residual: dihedral pdb=" CA VAL A 153 " pdb=" C VAL A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual -180.00 -108.33 -71.67 0 5.00e+00 4.00e-02 2.05e+02 dihedral pdb=" CA ILE H 167 " pdb=" C ILE H 167 " pdb=" N THR H 168 " pdb=" CA THR H 168 " ideal model delta harmonic sigma weight residual -180.00 -122.05 -57.95 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -124.81 -55.19 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 32183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4050 0.061 - 0.122: 1326 0.122 - 0.183: 222 0.183 - 0.244: 41 0.244 - 0.305: 9 Chirality restraints: 5648 Sorted by residual: chirality pdb=" CG LEU F 471 " pdb=" CB LEU F 471 " pdb=" CD1 LEU F 471 " pdb=" CD2 LEU F 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ALA D 178 " pdb=" N ALA D 178 " pdb=" C ALA D 178 " pdb=" CB ALA D 178 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5645 not shown) Planarity restraints: 9932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1034 " -0.828 9.50e-02 1.11e+02 2.76e-01 8.07e+01 pdb=" NE ARG C1034 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C1034 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C1034 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C1034 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG C1034 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG C1034 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG C1034 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C1034 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 178 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 179 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 128 " -0.043 2.00e-02 2.50e+03 2.54e-02 1.45e+01 pdb=" CG HIS B 128 " 0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS B 128 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS B 128 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS B 128 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS B 128 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS B 128 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 HIS B 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 9929 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2968 2.15 - 2.76: 136068 2.76 - 3.38: 199063 3.38 - 3.99: 252510 3.99 - 4.60: 385809 Nonbonded interactions: 976418 Sorted by model distance: nonbonded pdb=" H ALA D1157 " pdb=" O ASP D1208 " model vdw 1.538 2.450 nonbonded pdb=" OD2 ASP C 14 " pdb="HH21 ARG C1156 " model vdw 1.546 2.450 nonbonded pdb=" O TYR C 291 " pdb=" HZ3 LYS C 295 " model vdw 1.577 2.450 nonbonded pdb=" O MET C 768 " pdb=" H ASP C 785 " model vdw 1.583 2.450 nonbonded pdb=" O THR D 161 " pdb=" H TYR D 165 " model vdw 1.592 2.450 ... (remaining 976413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'G' and (resid 9 through 113 or (resid 114 and (name N or name CA or name \ C or name O or name CB or name CG or name SD or name CE or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or res \ id 115 through 205 or resid 301)) selection = (chain 'H' and (resid 9 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) or \ resid 124 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 o \ r name HD3 or name HE or name HH11 or name HH12 or name HH21)) or resid 170 thro \ ugh 205 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.920 Extract box with map and model: 2.020 Check model and map are aligned: 0.400 Set scattering table: 0.470 Process input model: 159.880 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1321 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 : 0.011 0.138 36242 Z= 0.712 Angle : 1.310 16.964 49608 Z= 0.728 Chirality : 0.061 0.305 5648 Planarity : 0.009 0.357 5910 Dihedral : 16.366 170.445 14327 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.69 % Allowed : 11.60 % Favored : 87.71 % Rotamer: Outliers : 0.26 % Allowed : 3.72 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.03 % Twisted Proline : 3.90 % Twisted General : 1.20 % 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: -4.55 (0.10), residues: 4060 helix: -2.89 (0.10), residues: 1485 sheet: -3.06 (0.23), residues: 377 loop : -3.17 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP H 85 HIS 0.025 0.004 HIS D 113 PHE 0.051 0.005 PHE D 763 TYR 0.057 0.005 TYR D 679 ARG 0.036 0.003 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 466 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 VAL cc_start: -0.0817 (p) cc_final: -0.1024 (p) REVERT: C 88 ARG cc_start: -0.0574 (mmp80) cc_final: -0.1569 (mtt180) REVERT: C 704 MET cc_start: -0.0606 (mmm) cc_final: -0.0957 (ttm) REVERT: C 1230 MET cc_start: -0.3302 (ttm) cc_final: -0.3555 (tpp) REVERT: D 614 LEU cc_start: 0.5529 (pt) cc_final: 0.5306 (pt) REVERT: D 625 MET cc_start: 0.4547 (ttp) cc_final: 0.4049 (tpp) REVERT: D 801 VAL cc_start: 0.6510 (t) cc_final: 0.6285 (t) REVERT: D 857 LEU cc_start: -0.0579 (OUTLIER) cc_final: -0.0794 (pp) REVERT: E 30 MET cc_start: -0.1666 (mtp) cc_final: -0.2779 (mmt) REVERT: F 456 MET cc_start: 0.4208 (mpt) cc_final: 0.3968 (mpp) REVERT: G 157 MET cc_start: -0.0569 (mpp) cc_final: -0.1145 (mpp) REVERT: H 157 MET cc_start: 0.0384 (mpp) cc_final: -0.0684 (mtt) outliers start: 9 outliers final: 7 residues processed: 474 average time/residue: 1.1562 time to fit residues: 840.8400 Evaluate side-chains 336 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 328 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 0.9990 chunk 316 optimal weight: 30.0000 chunk 175 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 327 optimal weight: 0.0050 chunk 126 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 379 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 46 GLN C 69 GLN C 148 GLN C 219 GLN C 339 ASN C 686 GLN C 688 GLN C1244 HIS C1288 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D 817 HIS D1023 HIS D1279 GLN D1350 ASN G 19 HIS H 65 ASN H 174 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1134 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 36242 Z= 0.252 Angle : 0.812 11.896 49608 Z= 0.444 Chirality : 0.046 0.263 5648 Planarity : 0.007 0.084 5910 Dihedral : 19.698 174.808 6234 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.21 % Favored : 90.22 % Rotamer: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 4060 helix: -1.89 (0.11), residues: 1561 sheet: -3.01 (0.23), residues: 395 loop : -2.87 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 183 HIS 0.014 0.002 HIS C1244 PHE 0.019 0.002 PHE C 934 TYR 0.036 0.002 TYR D 679 ARG 0.017 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.2396 (mmt) cc_final: -0.2818 (tpp) REVERT: C 88 ARG cc_start: -0.0977 (mmp80) cc_final: -0.2052 (mmt180) REVERT: C 369 MET cc_start: 0.7422 (ptm) cc_final: 0.7130 (tpt) REVERT: C 704 MET cc_start: -0.1099 (mmm) cc_final: -0.1440 (mtt) REVERT: C 1230 MET cc_start: -0.3344 (ttm) cc_final: -0.3685 (tpp) REVERT: D 801 VAL cc_start: 0.6206 (t) cc_final: 0.5999 (t) REVERT: E 30 MET cc_start: -0.1811 (mtp) cc_final: -0.2815 (mmt) REVERT: G 157 MET cc_start: -0.0085 (mpp) cc_final: -0.0926 (mpp) REVERT: H 157 MET cc_start: -0.0195 (mpp) cc_final: -0.1172 (mtt) outliers start: 2 outliers final: 1 residues processed: 384 average time/residue: 1.1308 time to fit residues: 667.8194 Evaluate side-chains 317 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 9.9990 chunk 117 optimal weight: 0.1980 chunk 315 optimal weight: 30.0000 chunk 258 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 380 optimal weight: 0.0370 chunk 410 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN H 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1100 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36242 Z= 0.211 Angle : 0.719 10.700 49608 Z= 0.394 Chirality : 0.044 0.219 5648 Planarity : 0.006 0.072 5910 Dihedral : 19.439 179.025 6234 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.80 % Rotamer: Outliers : 0.03 % Allowed : 1.51 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.25 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.12), residues: 4060 helix: -1.18 (0.12), residues: 1573 sheet: -2.81 (0.24), residues: 371 loop : -2.74 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.006 0.001 HIS D 777 PHE 0.018 0.002 PHE D 620 TYR 0.032 0.002 TYR D 679 ARG 0.007 0.000 ARG D1304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6941 (mt) cc_final: 0.6677 (pp) REVERT: B 51 MET cc_start: -0.2415 (mmp) cc_final: -0.2890 (tpp) REVERT: C 88 ARG cc_start: -0.1151 (mmp80) cc_final: -0.2007 (mtt90) REVERT: C 101 ARG cc_start: 0.5231 (ttm110) cc_final: 0.4873 (ttm170) REVERT: C 361 SER cc_start: 0.5172 (t) cc_final: 0.4881 (p) REVERT: C 704 MET cc_start: -0.1180 (mmm) cc_final: -0.1636 (mtt) REVERT: E 30 MET cc_start: -0.2042 (mtp) cc_final: -0.3074 (mmt) REVERT: G 157 MET cc_start: 0.0021 (mpp) cc_final: -0.0814 (mpp) REVERT: H 157 MET cc_start: -0.0226 (mpp) cc_final: -0.1222 (mtt) outliers start: 1 outliers final: 1 residues processed: 376 average time/residue: 1.0816 time to fit residues: 620.2821 Evaluate side-chains 318 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 381 optimal weight: 0.7980 chunk 404 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 23 HIS C1017 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 716 GLN D 865 HIS D1350 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1347 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36242 Z= 0.291 Angle : 0.753 11.707 49608 Z= 0.415 Chirality : 0.044 0.197 5648 Planarity : 0.006 0.112 5910 Dihedral : 19.428 178.796 6234 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.99 % Favored : 88.65 % Rotamer: Outliers : 0.03 % Allowed : 1.89 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.25 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.12), residues: 4060 helix: -0.98 (0.12), residues: 1577 sheet: -2.93 (0.23), residues: 394 loop : -2.76 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1193 HIS 0.007 0.002 HIS B 37 PHE 0.019 0.002 PHE C 225 TYR 0.028 0.002 TYR D 679 ARG 0.017 0.001 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1230 MET cc_start: -0.1496 (tpp) cc_final: -0.4044 (tpt) REVERT: G 157 MET cc_start: 0.0401 (mpp) cc_final: -0.0369 (mpp) REVERT: H 157 MET cc_start: -0.0016 (mpp) cc_final: -0.1018 (mtt) outliers start: 1 outliers final: 1 residues processed: 361 average time/residue: 1.0537 time to fit residues: 586.9081 Evaluate side-chains 311 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 0.0670 chunk 229 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1311 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36242 Z= 0.227 Angle : 0.701 11.662 49608 Z= 0.384 Chirality : 0.043 0.208 5648 Planarity : 0.006 0.097 5910 Dihedral : 19.371 179.443 6234 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.49 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.54 % 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: -2.81 (0.12), residues: 4060 helix: -0.72 (0.12), residues: 1578 sheet: -2.85 (0.24), residues: 377 loop : -2.64 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.009 0.001 HIS D1366 PHE 0.020 0.002 PHE H 102 TYR 0.019 0.002 TYR C 555 ARG 0.012 0.001 ARG F 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 3.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.6993 (mt) cc_final: 0.6776 (pp) REVERT: C 804 PHE cc_start: 0.2834 (m-80) cc_final: 0.2615 (m-80) REVERT: C 1230 MET cc_start: -0.1494 (tpp) cc_final: -0.3939 (tpt) REVERT: D 797 THR cc_start: 0.7744 (p) cc_final: 0.7416 (p) REVERT: G 157 MET cc_start: 0.0456 (mpp) cc_final: -0.0340 (mpp) REVERT: H 157 MET cc_start: -0.0020 (mpp) cc_final: -0.1080 (mtt) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 1.0490 time to fit residues: 572.3331 Evaluate side-chains 302 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 9.9990 chunk 363 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 404 optimal weight: 30.0000 chunk 335 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 133 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C1023 HIS C1116 HIS C1288 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1367 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36242 Z= 0.238 Angle : 0.690 11.435 49608 Z= 0.378 Chirality : 0.043 0.212 5648 Planarity : 0.005 0.080 5910 Dihedral : 19.318 176.926 6234 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.11 % Favored : 88.65 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.41 % 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: -2.68 (0.12), residues: 4060 helix: -0.51 (0.12), residues: 1576 sheet: -2.77 (0.25), residues: 353 loop : -2.68 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.013 0.001 HIS C1023 PHE 0.014 0.002 PHE D 620 TYR 0.020 0.002 TYR F 430 ARG 0.010 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: -0.0378 (ttm) cc_final: -0.0680 (ttm) REVERT: B 51 MET cc_start: -0.1910 (mmt) cc_final: -0.2212 (tpp) REVERT: C 1170 MET cc_start: 0.1768 (tmm) cc_final: 0.1557 (tmm) REVERT: C 1230 MET cc_start: -0.1614 (tpp) cc_final: -0.3967 (tpt) REVERT: D 797 THR cc_start: 0.7715 (p) cc_final: 0.7284 (p) REVERT: G 157 MET cc_start: 0.0447 (mpp) cc_final: -0.0287 (mpp) REVERT: H 157 MET cc_start: 0.0509 (mpp) cc_final: -0.0571 (mtt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 1.0275 time to fit residues: 538.1272 Evaluate side-chains 299 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 225 optimal weight: 0.0270 chunk 402 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 688 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1263 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36242 Z= 0.189 Angle : 0.658 11.065 49608 Z= 0.360 Chirality : 0.043 0.242 5648 Planarity : 0.005 0.076 5910 Dihedral : 19.212 175.524 6234 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.43 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.25 % Twisted General : 0.33 % 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: -2.46 (0.12), residues: 4060 helix: -0.30 (0.13), residues: 1568 sheet: -2.70 (0.25), residues: 365 loop : -2.55 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.010 0.001 HIS D1366 PHE 0.017 0.002 PHE D 620 TYR 0.035 0.002 TYR C 179 ARG 0.010 0.000 ARG F 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 51 MET cc_start: -0.2029 (mmt) cc_final: -0.2387 (tpp) REVERT: C 1230 MET cc_start: -0.1694 (tpp) cc_final: -0.3988 (tpt) REVERT: D 697 MET cc_start: -0.0003 (ppp) cc_final: -0.0524 (ppp) REVERT: D 698 MET cc_start: 0.2623 (tpp) cc_final: 0.1861 (mmt) REVERT: D 797 THR cc_start: 0.7569 (p) cc_final: 0.7173 (p) REVERT: G 157 MET cc_start: 0.0471 (mpp) cc_final: -0.0025 (mpp) REVERT: H 157 MET cc_start: 0.0522 (mpp) cc_final: -0.0583 (mtt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 1.0525 time to fit residues: 563.0873 Evaluate side-chains 297 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 30.0000 chunk 160 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 274 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C1013 GLN C1017 GLN C1023 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 346 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1521 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 36242 Z= 0.305 Angle : 0.738 11.682 49608 Z= 0.405 Chirality : 0.044 0.208 5648 Planarity : 0.006 0.075 5910 Dihedral : 19.292 174.820 6234 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.90 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.36 % 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: -2.69 (0.12), residues: 4060 helix: -0.51 (0.13), residues: 1569 sheet: -2.83 (0.24), residues: 390 loop : -2.65 (0.12), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.008 0.001 HIS C1023 PHE 0.017 0.002 PHE D 141 TYR 0.051 0.003 TYR F 430 ARG 0.016 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 51 MET cc_start: -0.1581 (mmt) cc_final: -0.2008 (tpp) REVERT: C 1230 MET cc_start: -0.1595 (tpp) cc_final: -0.3838 (tpt) REVERT: D 797 THR cc_start: 0.7718 (p) cc_final: 0.7496 (p) REVERT: E 30 MET cc_start: -0.1130 (mtt) cc_final: -0.1726 (mtp) REVERT: H 157 MET cc_start: 0.0948 (mpp) cc_final: -0.0239 (mtt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 1.0873 time to fit residues: 548.9733 Evaluate side-chains 298 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 5.9990 chunk 385 optimal weight: 30.0000 chunk 352 optimal weight: 2.9990 chunk 375 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 355 optimal weight: 8.9990 chunk 374 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1714 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 36242 Z= 0.357 Angle : 0.814 12.870 49608 Z= 0.447 Chirality : 0.048 0.502 5648 Planarity : 0.007 0.166 5910 Dihedral : 19.614 176.670 6234 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.10 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.12), residues: 4060 helix: -0.94 (0.12), residues: 1561 sheet: -3.07 (0.24), residues: 366 loop : -2.90 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 434 HIS 0.019 0.002 HIS D1366 PHE 0.041 0.003 PHE D 338 TYR 0.039 0.003 TYR D1241 ARG 0.044 0.001 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.1704 (mmt) cc_final: -0.2243 (mmt) REVERT: C 1230 MET cc_start: -0.1340 (tpp) cc_final: -0.3611 (tpt) REVERT: D 797 THR cc_start: 0.7922 (p) cc_final: 0.7639 (p) REVERT: E 30 MET cc_start: -0.0694 (mtt) cc_final: -0.1365 (mtp) REVERT: H 157 MET cc_start: 0.1487 (mpp) cc_final: 0.0370 (mtt) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 1.2211 time to fit residues: 616.8406 Evaluate side-chains 288 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1714 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 36242 Z= 0.322 Angle : 0.778 11.288 49608 Z= 0.426 Chirality : 0.045 0.322 5648 Planarity : 0.006 0.117 5910 Dihedral : 19.617 175.293 6234 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.96 % Favored : 86.82 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 4060 helix: -0.92 (0.12), residues: 1559 sheet: -3.14 (0.24), residues: 371 loop : -2.93 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1020 HIS 0.009 0.001 HIS D1218 PHE 0.022 0.002 PHE C 225 TYR 0.043 0.003 TYR F 430 ARG 0.014 0.001 ARG C 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1119 MET cc_start: -0.2176 (ttt) cc_final: -0.3105 (ttt) REVERT: C 1206 THR cc_start: 0.5954 (m) cc_final: 0.5729 (m) REVERT: C 1230 MET cc_start: -0.1294 (tpp) cc_final: -0.3509 (tpt) REVERT: D 797 THR cc_start: 0.7792 (p) cc_final: 0.7547 (p) REVERT: E 30 MET cc_start: -0.0879 (mtt) cc_final: -0.1582 (mtp) REVERT: H 157 MET cc_start: 0.1490 (mpp) cc_final: 0.0526 (mtt) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 1.0333 time to fit residues: 518.0482 Evaluate side-chains 290 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN C1116 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.133521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.110928 restraints weight = 1397242.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.110923 restraints weight = 1382352.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.110923 restraints weight = 1380700.659| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.6903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 36242 Z= 0.271 Angle : 0.735 10.932 49608 Z= 0.403 Chirality : 0.045 0.306 5648 Planarity : 0.006 0.082 5910 Dihedral : 19.590 173.848 6234 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.71 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.12), residues: 4060 helix: -0.78 (0.12), residues: 1557 sheet: -3.13 (0.25), residues: 348 loop : -2.89 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 85 HIS 0.008 0.001 HIS D 777 PHE 0.019 0.002 PHE D 338 TYR 0.039 0.002 TYR F 430 ARG 0.008 0.001 ARG D 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13156.04 seconds wall clock time: 226 minutes 45.70 seconds (13605.70 seconds total)