Starting phenix.real_space_refine on Thu Sep 26 00:59:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/09_2024/6pmj_20395_trim.cif" } resolution = 3.91 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= 0.289 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 113 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 18042 2.51 5 N 5218 2.21 5 O 5889 1.98 5 H 28609 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 57984 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} 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: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 21010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21010 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: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3871 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "1" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1712 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1724 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ATP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="ATP 3 1 " pdbres=" A 3 2 " 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 76.218 120.159 81.133 1.00 20.00 S ATOM 29466 SG CYS D 85 79.796 121.605 79.994 1.00 20.00 S ATOM 41046 SG CYS D 814 102.032 70.512 133.648 1.00 20.00 S ATOM 42183 SG CYS D 888 99.178 70.554 131.686 1.00 20.00 S ATOM 42274 SG CYS D 895 103.449 69.053 130.838 1.00 20.00 S Time building chain proxies: 21.57, per 1000 atoms: 0.37 Number of scatterers: 57984 At special positions: 0 Unit cell: (171, 149.4, 180.9, 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 110 16.00 P 113 15.00 Mg 1 11.99 O 5889 8.00 N 5218 7.00 C 18042 6.00 H 28609 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " 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 " 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6386 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 50 sheets defined 39.9% alpha, 13.3% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 23.32 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.698A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.688A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.686A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.005A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.170A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.791A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.717A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.751A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.280A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.760A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 493 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.665A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.638A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.502A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.522A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 4.069A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.147A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1038 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.778A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.803A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.792A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1261 through 1265 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.890A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 4.075A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.669A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.500A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.798A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.755A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.964A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.749A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 4.297A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 4.068A 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 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.727A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.739A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (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: 3.963A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.611A pdb=" N GLN D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 538 removed outlier: 3.882A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.661A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 removed outlier: 3.514A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 4.072A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 650 through 671 Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 788 removed outlier: 4.472A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.812A pdb=" N SER D 793 " --> pdb=" O LYS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.870A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 931 Proline residue: D 926 - end of helix removed outlier: 4.587A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR D 931 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.767A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.120A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.570A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D1258 " --> pdb=" O GLU D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1288 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.666A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1321 through 1326 removed outlier: 4.280A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1321 through 1326' Processing helix chain 'D' and resid 1327 through 1337 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.713A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.851A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.938A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.726A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 4.016A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 removed outlier: 3.503A pdb=" N VAL F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 41 through 58 removed outlier: 3.505A pdb=" N ARG F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 87 removed outlier: 4.285A pdb=" N GLN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 112 removed outlier: 3.965A pdb=" N ARG F 94 " --> pdb=" O PRO F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 127 through 139 removed outlier: 4.196A pdb=" N TYR F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 187 removed outlier: 4.449A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 173 " --> pdb=" O PRO F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.718A pdb=" N GLY F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 4.081A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 25 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 4.081A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.758A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.124A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.153A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.572A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.751A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 67 removed outlier: 5.278A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.675A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.990A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 249 through 250 removed outlier: 4.419A pdb=" N GLU C 249 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.910A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 598 through 599 Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 638 Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.044A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 798 through 803 Processing sheet with id=AC9, first strand: chain 'C' and resid 1076 through 1079 removed outlier: 7.986A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AD2, first strand: chain 'C' and resid 835 through 841 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 876 through 878 Processing sheet with id=AD5, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.246A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.860A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.860A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD9, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AE1, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.528A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE3, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE4, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AE5, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AE6, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE7, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.617A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.380A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.533A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF2, first strand: chain 'D' and resid 1025 through 1029 removed outlier: 4.591A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR D1029 " --> pdb=" O THR D1120 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR D1120 " --> pdb=" O THR D1029 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1079 through 1081 removed outlier: 4.066A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1047 through 1049 removed outlier: 4.387A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1177 through 1178 removed outlier: 3.721A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 24.17 Time building geometry restraints manager: 15.18 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: 28585 1.01 - 1.21: 27 1.21 - 1.41: 12044 1.41 - 1.61: 17793 1.61 - 1.81: 205 Bond restraints: 58654 Sorted by residual: bond pdb=" CA VAL D 997 " pdb=" C VAL D 997 " ideal model delta sigma weight residual 1.522 1.589 -0.067 7.10e-03 1.98e+04 8.97e+01 bond pdb=" CA PRO D 584 " pdb=" CB PRO D 584 " ideal model delta sigma weight residual 1.531 1.628 -0.097 1.22e-02 6.72e+03 6.27e+01 bond pdb=" C4 ATP 3 1 " pdb=" C5 ATP 3 1 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C5 ATP 3 1 " pdb=" C6 ATP 3 1 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.63e+01 bond pdb=" C5 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 58649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 105914 4.49 - 8.98: 439 8.98 - 13.47: 12 13.47 - 17.96: 1 17.96 - 22.45: 2 Bond angle restraints: 106368 Sorted by residual: angle pdb=" PB ATP 3 1 " pdb=" O3B ATP 3 1 " pdb=" PG ATP 3 1 " ideal model delta sigma weight residual 139.87 117.42 22.45 1.00e+00 1.00e+00 5.04e+02 angle pdb=" PA ATP 3 1 " pdb=" O3A ATP 3 1 " pdb=" PB ATP 3 1 " ideal model delta sigma weight residual 136.83 118.77 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" C5 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N3 ATP 3 1 " ideal model delta sigma weight residual 126.80 116.96 9.84 1.00e+00 1.00e+00 9.68e+01 angle pdb=" N3 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N9 ATP 3 1 " ideal model delta sigma weight residual 127.04 136.69 -9.65 1.15e+00 7.59e-01 7.07e+01 angle pdb=" C LEU F 31 " pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 123.04 131.24 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 106363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 25666 35.91 - 71.82: 1142 71.82 - 107.73: 18 107.73 - 143.64: 1 143.64 - 179.56: 9 Dihedral angle restraints: 26836 sinusoidal: 15840 harmonic: 10996 Sorted by residual: dihedral pdb=" CA ASP D 67 " pdb=" C ASP D 67 " pdb=" N TYR D 68 " pdb=" CA TYR D 68 " ideal model delta harmonic sigma weight residual -180.00 -114.16 -65.84 0 5.00e+00 4.00e-02 1.73e+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 -128.50 -51.50 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA GLU F 151 " pdb=" C GLU F 151 " pdb=" N GLU F 152 " pdb=" CA GLU F 152 " ideal model delta harmonic sigma weight residual -180.00 -130.72 -49.28 0 5.00e+00 4.00e-02 9.71e+01 ... (remaining 26833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3736 0.076 - 0.151: 851 0.151 - 0.227: 84 0.227 - 0.303: 3 0.303 - 0.378: 1 Chirality restraints: 4675 Sorted by residual: chirality pdb=" CB VAL D 65 " pdb=" CA VAL D 65 " pdb=" CG1 VAL D 65 " pdb=" CG2 VAL D 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CG LEU C 971 " pdb=" CB LEU C 971 " pdb=" CD1 LEU C 971 " pdb=" CD2 LEU C 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 80 " pdb=" CB LEU F 80 " pdb=" CD1 LEU F 80 " pdb=" CD2 LEU F 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4672 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 68 " -0.018 2.00e-02 2.50e+03 3.71e-02 4.14e+01 pdb=" CG TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 68 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 68 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 68 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 68 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR D 68 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TYR D 68 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR D 68 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR D 68 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR D 68 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 47 " 0.034 2.00e-02 2.50e+03 1.92e-02 1.10e+01 pdb=" N1 DT 1 47 " -0.038 2.00e-02 2.50e+03 pdb=" C2 DT 1 47 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT 1 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT 1 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT 1 47 " 0.023 2.00e-02 2.50e+03 pdb=" O4 DT 1 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT 1 47 " 0.025 2.00e-02 2.50e+03 pdb=" C7 DT 1 47 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DT 1 47 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT 1 47 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT 1 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 795 " -0.001 2.00e-02 2.50e+03 1.89e-02 1.07e+01 pdb=" CG TYR D 795 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR D 795 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 795 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 795 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 795 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 795 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR D 795 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR D 795 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR D 795 " 0.001 2.00e-02 2.50e+03 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 2449 2.14 - 2.76: 113813 2.76 - 3.37: 162494 3.37 - 3.99: 205259 3.99 - 4.60: 314840 Nonbonded interactions: 798855 Sorted by model distance: nonbonded pdb=" HB3 LYS D 87 " pdb=" HZ3 LYS D 87 " model vdw 1.528 2.270 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.592 2.450 nonbonded pdb=" O SER F 219 " pdb=" HG SER F 222 " model vdw 1.615 2.450 nonbonded pdb=" OE2 GLU A 214 " pdb=" HE ARG A 218 " model vdw 1.619 2.450 nonbonded pdb=" O GLN C 618 " pdb=" HG SER C 621 " model vdw 1.624 2.450 ... (remaining 798850 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' } 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: 3.140 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: 0.810 Extract box with map and model: 1.960 Check model and map are aligned: 0.380 Set scattering table: 0.430 Process input model: 138.870 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.190 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 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 0.097 30045 Z= 0.706 Angle : 1.211 22.446 41067 Z= 0.709 Chirality : 0.061 0.378 4675 Planarity : 0.007 0.080 4992 Dihedral : 16.103 179.555 11826 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer: Outliers : 0.31 % Allowed : 4.93 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.30 % 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: -4.41 (0.11), residues: 3437 helix: -2.49 (0.11), residues: 1202 sheet: -3.35 (0.21), residues: 344 loop : -3.23 (0.12), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 149 HIS 0.023 0.004 HIS F 14 PHE 0.042 0.004 PHE C 505 TYR 0.065 0.005 TYR D 68 ARG 0.029 0.002 ARG D 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 557 time to evaluate : 3.534 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4784 (tmt) cc_final: 0.4563 (tmm) REVERT: C 82 VAL cc_start: 0.6072 (t) cc_final: 0.5726 (t) REVERT: D 917 VAL cc_start: 0.5794 (t) cc_final: 0.5515 (t) outliers start: 9 outliers final: 4 residues processed: 564 average time/residue: 1.0507 time to fit residues: 864.7594 Evaluate side-chains 374 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 370 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 834 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN C 36 GLN C 83 GLN C1157 GLN D 341 ASN D 560 ASN D 667 GLN E 15 ASN E 61 ASN F 32 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4390 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30045 Z= 0.231 Angle : 0.752 11.103 41067 Z= 0.414 Chirality : 0.045 0.178 4675 Planarity : 0.006 0.066 4992 Dihedral : 18.658 175.625 5057 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.00 % Favored : 91.82 % Rotamer: Outliers : 1.32 % Allowed : 10.43 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.15 % 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: -3.43 (0.12), residues: 3437 helix: -1.30 (0.13), residues: 1255 sheet: -2.96 (0.23), residues: 332 loop : -2.93 (0.12), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 17 HIS 0.006 0.001 HIS C 343 PHE 0.024 0.002 PHE C1265 TYR 0.023 0.002 TYR D 68 ARG 0.014 0.001 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 412 time to evaluate : 3.847 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 433 average time/residue: 1.0229 time to fit residues: 635.5433 Evaluate side-chains 374 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 345 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 320 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 0.0040 chunk 317 optimal weight: 0.0170 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 overall best weight: 4.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 805 GLN F 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4536 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30045 Z= 0.249 Angle : 0.700 10.666 41067 Z= 0.385 Chirality : 0.043 0.168 4675 Planarity : 0.005 0.063 4992 Dihedral : 18.282 174.855 5050 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.70 % Favored : 91.13 % Rotamer: Outliers : 1.53 % Allowed : 12.43 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -2.95 (0.13), residues: 3437 helix: -0.81 (0.14), residues: 1263 sheet: -2.59 (0.22), residues: 399 loop : -2.72 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 17 HIS 0.009 0.001 HIS C1237 PHE 0.018 0.002 PHE C 186 TYR 0.024 0.002 TYR D 68 ARG 0.009 0.001 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 354 time to evaluate : 3.588 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 138 ILE cc_start: 0.6396 (mm) cc_final: 0.6078 (pt) REVERT: C 667 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5482 (tt) REVERT: C 1273 MET cc_start: 0.6939 (mpp) cc_final: 0.6688 (mpp) outliers start: 45 outliers final: 34 residues processed: 376 average time/residue: 1.0430 time to fit residues: 560.6691 Evaluate side-chains 364 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 329 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 1233 ILE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 225 HIS Chi-restraints excluded: chain F residue 229 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 30.0000 chunk 240 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 340 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 767 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 341 ASN D 665 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30045 Z= 0.266 Angle : 0.703 10.070 41067 Z= 0.388 Chirality : 0.044 0.223 4675 Planarity : 0.005 0.092 4992 Dihedral : 18.235 175.588 5050 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.11 % Favored : 90.72 % Rotamer: Outliers : 2.34 % Allowed : 12.77 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.15 % 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: -2.64 (0.13), residues: 3437 helix: -0.57 (0.14), residues: 1271 sheet: -2.19 (0.24), residues: 381 loop : -2.62 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 17 HIS 0.006 0.002 HIS F 14 PHE 0.017 0.002 PHE C1265 TYR 0.026 0.002 TYR C 179 ARG 0.007 0.001 ARG C1301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 326 time to evaluate : 3.862 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: C 667 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5641 (tt) outliers start: 69 outliers final: 55 residues processed: 367 average time/residue: 1.0123 time to fit residues: 535.5815 Evaluate side-chains 352 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 296 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 30.0000 chunk 193 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4830 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30045 Z= 0.320 Angle : 0.731 10.089 41067 Z= 0.403 Chirality : 0.044 0.162 4675 Planarity : 0.006 0.066 4992 Dihedral : 18.310 176.775 5050 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.45 % Favored : 89.38 % Rotamer: Outliers : 2.96 % Allowed : 13.79 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.76 (0.13), residues: 3437 helix: -0.69 (0.14), residues: 1279 sheet: -2.14 (0.24), residues: 396 loop : -2.69 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D1193 HIS 0.012 0.002 HIS C1023 PHE 0.017 0.002 PHE C 505 TYR 0.022 0.002 TYR D 537 ARG 0.021 0.001 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 299 time to evaluate : 3.583 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: C 1273 MET cc_start: 0.7355 (mpp) cc_final: 0.7145 (mpp) REVERT: D 69 GLU cc_start: 0.4497 (mp0) cc_final: 0.4282 (mp0) REVERT: D 180 MET cc_start: 0.4405 (ttp) cc_final: 0.3828 (ttp) REVERT: D 192 MET cc_start: 0.2818 (ttp) cc_final: 0.2534 (ttp) outliers start: 87 outliers final: 71 residues processed: 354 average time/residue: 1.0041 time to fit residues: 514.9487 Evaluate side-chains 353 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 282 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 0.9980 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30045 Z= 0.292 Angle : 0.713 9.716 41067 Z= 0.392 Chirality : 0.044 0.158 4675 Planarity : 0.006 0.080 4992 Dihedral : 18.292 177.234 5050 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.78 % Favored : 90.05 % Rotamer: Outliers : 2.89 % Allowed : 15.35 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.15 % 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 (0.13), residues: 3437 helix: -0.61 (0.14), residues: 1281 sheet: -2.18 (0.24), residues: 396 loop : -2.65 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1193 HIS 0.006 0.002 HIS A 66 PHE 0.017 0.002 PHE D 141 TYR 0.018 0.002 TYR A 68 ARG 0.015 0.001 ARG D1290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 290 time to evaluate : 3.594 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: C 124 MET cc_start: 0.4839 (ppp) cc_final: 0.4340 (ppp) REVERT: D 192 MET cc_start: 0.3045 (ttp) cc_final: 0.2819 (ttp) outliers start: 85 outliers final: 76 residues processed: 343 average time/residue: 0.9685 time to fit residues: 489.2029 Evaluate side-chains 346 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 270 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1175 ASN Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 192 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 339 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30045 Z= 0.301 Angle : 0.713 9.255 41067 Z= 0.391 Chirality : 0.044 0.161 4675 Planarity : 0.006 0.084 4992 Dihedral : 18.276 178.010 5050 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 3.02 % Allowed : 16.17 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -2.75 (0.13), residues: 3437 helix: -0.66 (0.14), residues: 1290 sheet: -2.13 (0.25), residues: 387 loop : -2.72 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1193 HIS 0.007 0.002 HIS B 23 PHE 0.018 0.002 PHE D 141 TYR 0.019 0.002 TYR A 68 ARG 0.014 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 274 time to evaluate : 3.505 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: C 124 MET cc_start: 0.4719 (ppp) cc_final: 0.4330 (ppp) REVERT: C 811 ASN cc_start: 0.3268 (OUTLIER) cc_final: 0.2293 (m-40) REVERT: D 192 MET cc_start: 0.3201 (ttp) cc_final: 0.2992 (ttp) outliers start: 89 outliers final: 80 residues processed: 333 average time/residue: 0.9712 time to fit residues: 480.0644 Evaluate side-chains 348 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 267 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1175 ASN Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4932 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30045 Z= 0.252 Angle : 0.675 8.917 41067 Z= 0.369 Chirality : 0.043 0.154 4675 Planarity : 0.005 0.069 4992 Dihedral : 18.232 177.489 5050 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.40 % Favored : 90.43 % Rotamer: Outliers : 2.82 % Allowed : 16.75 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % 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: -2.61 (0.13), residues: 3437 helix: -0.54 (0.14), residues: 1292 sheet: -2.08 (0.25), residues: 398 loop : -2.64 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 580 HIS 0.007 0.001 HIS B 23 PHE 0.017 0.002 PHE C 385 TYR 0.017 0.002 TYR D 165 ARG 0.011 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 276 time to evaluate : 3.524 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: C 124 MET cc_start: 0.4815 (ppp) cc_final: 0.4462 (ppp) REVERT: C 896 THR cc_start: 0.2518 (OUTLIER) cc_final: 0.2240 (p) REVERT: D 192 MET cc_start: 0.3329 (ttp) cc_final: 0.3113 (ttp) REVERT: D 428 THR cc_start: 0.2411 (OUTLIER) cc_final: 0.2169 (m) outliers start: 83 outliers final: 75 residues processed: 333 average time/residue: 0.9639 time to fit residues: 476.3940 Evaluate side-chains 346 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 269 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1175 ASN Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 225 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5069 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30045 Z= 0.351 Angle : 0.751 9.069 41067 Z= 0.414 Chirality : 0.045 0.160 4675 Planarity : 0.006 0.067 4992 Dihedral : 18.401 179.758 5048 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.63 % Favored : 87.20 % Rotamer: Outliers : 2.96 % Allowed : 16.98 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -2.92 (0.13), residues: 3437 helix: -0.85 (0.14), residues: 1296 sheet: -2.34 (0.25), residues: 393 loop : -2.75 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1193 HIS 0.007 0.002 HIS F 14 PHE 0.018 0.002 PHE C 385 TYR 0.023 0.002 TYR D 537 ARG 0.010 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 267 time to evaluate : 3.540 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: C 124 MET cc_start: 0.4961 (ppp) cc_final: 0.4623 (ppp) REVERT: C 811 ASN cc_start: 0.3822 (OUTLIER) cc_final: 0.2643 (m-40) REVERT: C 896 THR cc_start: 0.2383 (OUTLIER) cc_final: 0.2146 (p) REVERT: D 192 MET cc_start: 0.3272 (ttp) cc_final: 0.3053 (ttp) REVERT: D 428 THR cc_start: 0.2243 (OUTLIER) cc_final: 0.2012 (m) outliers start: 87 outliers final: 79 residues processed: 330 average time/residue: 0.9649 time to fit residues: 476.3176 Evaluate side-chains 341 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 259 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1175 ASN Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1242 ARG Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 334 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 350 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5014 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30045 Z= 0.265 Angle : 0.693 8.373 41067 Z= 0.379 Chirality : 0.043 0.158 4675 Planarity : 0.005 0.078 4992 Dihedral : 18.365 178.085 5048 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.83 % Favored : 90.02 % Rotamer: Outliers : 2.82 % Allowed : 17.32 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -2.75 (0.13), residues: 3437 helix: -0.71 (0.14), residues: 1303 sheet: -2.25 (0.25), residues: 400 loop : -2.65 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 580 HIS 0.008 0.001 HIS B 23 PHE 0.014 0.002 PHE C 385 TYR 0.016 0.002 TYR F 131 ARG 0.010 0.001 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 270 time to evaluate : 3.542 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: C 124 MET cc_start: 0.4904 (ppp) cc_final: 0.4578 (ppp) REVERT: C 811 ASN cc_start: 0.3574 (OUTLIER) cc_final: 0.2562 (m-40) REVERT: C 896 THR cc_start: 0.2305 (OUTLIER) cc_final: 0.2069 (p) REVERT: D 192 MET cc_start: 0.3280 (ttp) cc_final: 0.3058 (ttp) REVERT: D 428 THR cc_start: 0.2403 (OUTLIER) cc_final: 0.2185 (m) outliers start: 83 outliers final: 78 residues processed: 330 average time/residue: 0.9241 time to fit residues: 452.5185 Evaluate side-chains 347 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 266 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 762 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1027 LYS Chi-restraints excluded: chain C residue 1030 GLU Chi-restraints excluded: chain C residue 1175 ASN Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 180 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 297 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.068351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.051929 restraints weight = 753689.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.054154 restraints weight = 433424.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.055690 restraints weight = 295120.687| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.7458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30045 Z= 0.204 Angle : 0.654 9.097 41067 Z= 0.354 Chirality : 0.043 0.194 4675 Planarity : 0.005 0.067 4992 Dihedral : 18.264 177.507 5048 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.63 % Favored : 90.22 % Rotamer: Outliers : 2.41 % Allowed : 17.76 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % 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: -2.38 (0.14), residues: 3437 helix: -0.34 (0.14), residues: 1285 sheet: -2.16 (0.25), residues: 393 loop : -2.45 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 580 HIS 0.007 0.001 HIS F 225 PHE 0.014 0.002 PHE C 514 TYR 0.013 0.002 TYR D 68 ARG 0.010 0.001 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11361.59 seconds wall clock time: 212 minutes 17.34 seconds (12737.34 seconds total)