Starting phenix.real_space_refine on Thu Sep 26 00:41:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/09_2024/6pmi_20394_trim.cif" } resolution = 3.86 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= -0.018 sd= 0.345 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 28610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 57985 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: 21011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21011 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 82.000 115.253 86.755 1.00 20.00 S ATOM 29237 SG CYS D 72 82.138 118.199 84.955 1.00 20.00 S ATOM 29467 SG CYS D 85 83.046 118.637 88.108 1.00 20.00 S ATOM 29514 SG CYS D 88 79.760 118.492 88.871 1.00 20.00 S ATOM 41047 SG CYS D 814 101.947 70.561 133.594 1.00 20.00 S ATOM 42184 SG CYS D 888 99.141 70.430 131.641 1.00 20.00 S ATOM 42275 SG CYS D 895 103.449 69.075 130.891 1.00 20.00 S Time building chain proxies: 21.40, per 1000 atoms: 0.37 Number of scatterers: 57985 At special positions: 0 Unit cell: (171.9, 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 28610 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: 12.30 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " 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 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 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: 119 helices and 46 sheets defined 40.1% alpha, 12.8% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 23.53 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.543A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.729A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.703A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.365A 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 86 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: 4.174A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.221A 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: 3.824A 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 329 removed outlier: 3.803A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.561A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.790A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.867A 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: 4.321A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.507A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 removed outlier: 3.847A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 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: 3.509A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 674' Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.623A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.757A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.565A 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: 3.688A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.922A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.838A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.822A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (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 removed outlier: 3.591A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) 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: 3.829A 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: 3.963A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.054A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 removed outlier: 3.778A 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: 3.989A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.918A 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 264 through 284 removed outlier: 3.522A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 4.074A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.623A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.936A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.790A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.907A 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 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.597A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.604A 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: 4.019A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 4.210A 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: 4.403A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 removed outlier: 3.821A pdb=" N SER D 793 " --> pdb=" O LYS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.745A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 928 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 929 through 931 No H-bonds generated for 'chain 'D' and resid 929 through 931' Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.780A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.274A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.626A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.668A 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: 4.073A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 4.083A pdb=" N PHE D1325 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1337 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.768A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1375 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.959A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.703A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 4.002A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 66 through 87 removed outlier: 4.251A pdb=" N GLN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 112 removed outlier: 4.150A 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: 3.913A pdb=" N TYR F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 187 removed outlier: 4.436A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 173 " --> pdb=" O PRO F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.578A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.720A pdb=" N GLY F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 213 " --> pdb=" O GLU F 209 " (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 18 removed outlier: 3.810A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.752A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.389A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.389A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.138A 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: 5.933A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.463A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.743A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU C 106 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS C 115 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.738A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.928A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 249 through 250 removed outlier: 4.377A pdb=" N GLU C 249 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.160A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 598 through 599 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 638 Processing sheet with id=AC3, first strand: chain 'C' and resid 750 through 752 removed outlier: 5.941A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1076 through 1079 removed outlier: 7.711A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 831 Processing sheet with id=AC8, first strand: chain 'C' and resid 835 through 841 Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.304A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.847A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.115A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AE1, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.631A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.715A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 991 through 995 removed outlier: 6.498A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'D' and resid 1028 through 1029 removed outlier: 3.883A pdb=" N ASP D1119 " --> pdb=" O THR D1029 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1079 through 1081 removed outlier: 4.091A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1047 through 1049 removed outlier: 4.366A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1106 through 1107 removed outlier: 3.738A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 24.56 Time building geometry restraints manager: 15.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 28588 1.02 - 1.22: 87 1.22 - 1.42: 12270 1.42 - 1.62: 17518 1.62 - 1.82: 192 Bond restraints: 58655 Sorted by residual: bond pdb=" C4 ATP 3 1 " pdb=" C5 ATP 3 1 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.58e+01 bond pdb=" C5 ATP 3 1 " pdb=" C6 ATP 3 1 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 bond pdb=" C5 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.63e+01 bond pdb=" C ARG D1148 " pdb=" N ARG D1149 " ideal model delta sigma weight residual 1.331 1.231 0.100 2.07e-02 2.33e+03 2.34e+01 bond pdb=" C8 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.85e+01 ... (remaining 58650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 105896 4.65 - 9.31: 457 9.31 - 13.96: 14 13.96 - 18.62: 0 18.62 - 23.27: 2 Bond angle restraints: 106369 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 139.87 116.60 23.27 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PA ATP 3 1 " pdb=" O3A ATP 3 1 " pdb=" PB ATP 3 1 " ideal model delta sigma weight residual 136.83 117.81 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" C5 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N3 ATP 3 1 " ideal model delta sigma weight residual 126.80 117.42 9.38 1.00e+00 1.00e+00 8.81e+01 angle pdb=" N3 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N9 ATP 3 1 " ideal model delta sigma weight residual 127.04 136.02 -8.98 1.15e+00 7.59e-01 6.12e+01 angle pdb=" N VAL F 33 " pdb=" CA VAL F 33 " pdb=" C VAL F 33 " ideal model delta sigma weight residual 109.34 121.94 -12.60 2.08e+00 2.31e-01 3.67e+01 ... (remaining 106364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 25629 35.69 - 71.39: 1181 71.39 - 107.08: 17 107.08 - 142.77: 1 142.77 - 178.46: 9 Dihedral angle restraints: 26837 sinusoidal: 15841 harmonic: 10996 Sorted by residual: 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 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+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 -130.73 -49.27 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA GLU B 76 " pdb=" C GLU B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta harmonic sigma weight residual 180.00 135.80 44.20 0 5.00e+00 4.00e-02 7.81e+01 ... (remaining 26834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3570 0.072 - 0.143: 950 0.143 - 0.215: 140 0.215 - 0.287: 14 0.287 - 0.359: 1 Chirality restraints: 4675 Sorted by residual: chirality pdb=" CB VAL C 98 " pdb=" CA VAL C 98 " pdb=" CG1 VAL C 98 " pdb=" CG2 VAL C 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+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 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE C1112 " pdb=" CA ILE C1112 " pdb=" CG1 ILE C1112 " pdb=" CG2 ILE C1112 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4672 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 68 " -0.016 2.00e-02 2.50e+03 2.27e-02 1.55e+01 pdb=" CG TYR D 68 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 68 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 68 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 68 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR D 68 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D 68 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR D 68 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR D 68 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR D 68 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR D 68 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR D 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 95 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR D 95 " 0.059 2.00e-02 2.50e+03 pdb=" O THR D 95 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS D 96 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO D 121 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.045 5.00e-02 4.00e+02 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 929 2.06 - 2.69: 97304 2.69 - 3.33: 169624 3.33 - 3.96: 210523 3.96 - 4.60: 324700 Nonbonded interactions: 803080 Sorted by model distance: nonbonded pdb=" O2 DC 1 87 " pdb=" H22 DG 2 2 " model vdw 1.419 2.450 nonbonded pdb=" H ASP C 624 " pdb=" O HIS C 628 " model vdw 1.573 2.450 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.580 2.450 nonbonded pdb=" OG SER C 61 " pdb=" H GLY C 64 " model vdw 1.599 2.450 nonbonded pdb=" HZ2 LYS D 850 " pdb=" O ASP D 855 " model vdw 1.603 2.450 ... (remaining 803075 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.780 Extract box with map and model: 1.840 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 139.270 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.200 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 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 : 0.012 0.106 30045 Z= 0.779 Angle : 1.261 23.269 41067 Z= 0.735 Chirality : 0.064 0.359 4675 Planarity : 0.007 0.083 4992 Dihedral : 16.098 178.463 11826 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.74 % Favored : 88.89 % Rotamer: Outliers : 0.24 % Allowed : 4.99 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.51 % 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: -4.48 (0.11), residues: 3437 helix: -2.55 (0.11), residues: 1193 sheet: -3.28 (0.23), residues: 316 loop : -3.31 (0.12), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 807 HIS 0.018 0.004 HIS B 23 PHE 0.034 0.004 PHE C 156 TYR 0.047 0.005 TYR D 68 ARG 0.031 0.003 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 543 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 536 time to evaluate : 3.467 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: C 912 ASP cc_start: 0.4912 (p0) cc_final: 0.4673 (p0) REVERT: C 1114 GLU cc_start: 0.5106 (pp20) cc_final: 0.4031 (pp20) REVERT: D 424 ASN cc_start: 0.6454 (t160) cc_final: 0.6214 (t0) REVERT: D 698 MET cc_start: 0.2384 (tpp) cc_final: 0.1817 (mmm) REVERT: D 917 VAL cc_start: 0.6801 (t) cc_final: 0.6506 (t) REVERT: F 151 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.1833 (tm-30) outliers start: 7 outliers final: 4 residues processed: 540 average time/residue: 1.0566 time to fit residues: 839.4863 Evaluate side-chains 372 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 367 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 834 PRO Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain F residue 151 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN C 36 GLN C 83 GLN C 604 HIS C 752 ASN C 894 GLN C1009 ASN C1017 GLN C1157 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN E 15 ASN F 14 HIS F 32 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5124 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30045 Z= 0.235 Angle : 0.762 11.157 41067 Z= 0.417 Chirality : 0.045 0.232 4675 Planarity : 0.006 0.080 4992 Dihedral : 18.684 175.758 5056 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.44 % Favored : 91.39 % Rotamer: Outliers : 1.60 % Allowed : 9.88 % Favored : 88.52 % 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: -3.46 (0.12), residues: 3437 helix: -1.41 (0.13), residues: 1261 sheet: -2.76 (0.24), residues: 320 loop : -2.94 (0.12), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1276 HIS 0.008 0.001 HIS D 430 PHE 0.025 0.002 PHE C 464 TYR 0.020 0.002 TYR D1282 ARG 0.010 0.001 ARG C 180 *********************** 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 469 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 422 time to evaluate : 3.516 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: C 1114 GLU cc_start: 0.4554 (pp20) cc_final: 0.4107 (tm-30) REVERT: D 473 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6813 (t) REVERT: D 698 MET cc_start: 0.2413 (tpp) cc_final: 0.2019 (mmm) REVERT: F 79 MET cc_start: 0.4960 (mmm) cc_final: 0.4614 (mmm) REVERT: F 151 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2334 (tm-30) REVERT: F 171 GLN cc_start: 0.4386 (mm-40) cc_final: 0.3978 (mm-40) outliers start: 47 outliers final: 26 residues processed: 448 average time/residue: 0.8856 time to fit residues: 596.3107 Evaluate side-chains 387 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 359 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 320 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 317 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 622 ASN C 725 GLN C1129 ASN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30045 Z= 0.374 Angle : 0.787 10.986 41067 Z= 0.435 Chirality : 0.045 0.166 4675 Planarity : 0.006 0.070 4992 Dihedral : 18.463 174.165 5053 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.77 % Favored : 89.00 % Rotamer: Outliers : 2.21 % Allowed : 11.41 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.24 % 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: -3.35 (0.13), residues: 3437 helix: -1.21 (0.13), residues: 1271 sheet: -2.54 (0.24), residues: 354 loop : -2.99 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 868 HIS 0.008 0.002 HIS F 153 PHE 0.024 0.002 PHE C 80 TYR 0.032 0.002 TYR D 795 ARG 0.018 0.001 ARG D 293 *********************** 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 413 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 3.465 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: C 1141 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5985 (mt) REVERT: C 1230 MET cc_start: 0.4558 (mmm) cc_final: 0.4199 (mmm) REVERT: D 473 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6748 (t) REVERT: D 895 CYS cc_start: 0.4003 (OUTLIER) cc_final: 0.2899 (p) REVERT: F 26 HIS cc_start: 0.3619 (OUTLIER) cc_final: 0.3316 (p-80) REVERT: F 79 MET cc_start: 0.5166 (mmm) cc_final: 0.4781 (mmm) outliers start: 65 outliers final: 48 residues processed: 385 average time/residue: 0.8646 time to fit residues: 513.8344 Evaluate side-chains 360 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 308 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 578 ILE 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 808 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 321 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN C 688 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30045 Z= 0.204 Angle : 0.672 9.983 41067 Z= 0.366 Chirality : 0.043 0.184 4675 Planarity : 0.005 0.066 4992 Dihedral : 18.300 174.626 5051 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.65 % Favored : 92.17 % Rotamer: Outliers : 1.80 % Allowed : 12.94 % Favored : 85.26 % 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: -2.83 (0.13), residues: 3437 helix: -0.69 (0.14), residues: 1272 sheet: -2.22 (0.25), residues: 341 loop : -2.77 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 17 HIS 0.005 0.001 HIS B 128 PHE 0.020 0.002 PHE C 464 TYR 0.042 0.002 TYR C1281 ARG 0.014 0.000 ARG D 293 *********************** 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 399 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 346 time to evaluate : 3.501 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: C 523 GLU cc_start: 0.5707 (mp0) cc_final: 0.5465 (mm-30) REVERT: D 473 THR cc_start: 0.6851 (OUTLIER) cc_final: 0.6581 (t) REVERT: F 79 MET cc_start: 0.5001 (mmm) cc_final: 0.4708 (mmm) outliers start: 53 outliers final: 39 residues processed: 377 average time/residue: 0.8399 time to fit residues: 484.3986 Evaluate side-chains 361 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 321 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 253 optimal weight: 40.0000 chunk 140 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 613 ASN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30045 Z= 0.349 Angle : 0.747 10.163 41067 Z= 0.413 Chirality : 0.044 0.161 4675 Planarity : 0.006 0.095 4992 Dihedral : 18.422 176.149 5048 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.46 % Favored : 88.30 % Rotamer: Outliers : 2.72 % Allowed : 13.45 % Favored : 83.83 % 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: -3.04 (0.13), residues: 3437 helix: -0.93 (0.14), residues: 1263 sheet: -2.17 (0.25), residues: 357 loop : -2.87 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 997 HIS 0.007 0.002 HIS D1366 PHE 0.018 0.002 PHE C 464 TYR 0.024 0.002 TYR F 20 ARG 0.010 0.001 ARG D 259 *********************** 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 394 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 314 time to evaluate : 3.468 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: C 678 ARG cc_start: 0.6711 (mmp80) cc_final: 0.6475 (mmp-170) REVERT: C 1232 MET cc_start: 0.5585 (ppp) cc_final: 0.5235 (ppp) REVERT: D 473 THR cc_start: 0.6960 (OUTLIER) cc_final: 0.6722 (t) REVERT: D 723 TYR cc_start: 0.5003 (OUTLIER) cc_final: 0.4766 (t80) REVERT: F 26 HIS cc_start: 0.4392 (OUTLIER) cc_final: 0.4042 (p-80) REVERT: F 79 MET cc_start: 0.5234 (mmm) cc_final: 0.4914 (mmm) outliers start: 80 outliers final: 67 residues processed: 375 average time/residue: 0.8331 time to fit residues: 481.9674 Evaluate side-chains 362 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 292 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 723 TYR Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 0.1980 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 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: 0.5362 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30045 Z= 0.183 Angle : 0.655 10.009 41067 Z= 0.354 Chirality : 0.042 0.166 4675 Planarity : 0.005 0.072 4992 Dihedral : 18.309 175.869 5048 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 1.73 % Allowed : 14.47 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.47 (0.13), residues: 3437 helix: -0.35 (0.14), residues: 1278 sheet: -2.02 (0.25), residues: 349 loop : -2.61 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 115 HIS 0.005 0.001 HIS D 430 PHE 0.022 0.001 PHE C 972 TYR 0.023 0.001 TYR F 20 ARG 0.015 0.000 ARG C1106 *********************** 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 378 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 327 time to evaluate : 3.491 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: C 628 HIS cc_start: 0.2557 (OUTLIER) cc_final: 0.1966 (p-80) REVERT: D 473 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6573 (t) REVERT: D 802 ASP cc_start: 0.4996 (t0) cc_final: 0.4261 (t0) REVERT: F 79 MET cc_start: 0.4982 (mmm) cc_final: 0.4775 (mmm) outliers start: 51 outliers final: 42 residues processed: 362 average time/residue: 0.8263 time to fit residues: 460.4806 Evaluate side-chains 343 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 299 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30045 Z= 0.415 Angle : 0.779 9.692 41067 Z= 0.433 Chirality : 0.045 0.176 4675 Planarity : 0.006 0.057 4992 Dihedral : 18.463 177.235 5048 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.10 % Favored : 87.69 % Rotamer: Outliers : 2.75 % Allowed : 15.05 % Favored : 82.20 % 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: -3.02 (0.13), residues: 3437 helix: -0.91 (0.14), residues: 1283 sheet: -2.13 (0.25), residues: 380 loop : -2.89 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 115 HIS 0.008 0.002 HIS D1366 PHE 0.025 0.002 PHE D1325 TYR 0.026 0.002 TYR D 723 ARG 0.011 0.001 ARG D 259 *********************** 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 361 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 280 time to evaluate : 3.494 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: C 628 HIS cc_start: 0.3176 (OUTLIER) cc_final: 0.2126 (p-80) REVERT: D 473 THR cc_start: 0.6975 (OUTLIER) cc_final: 0.6685 (t) REVERT: D 536 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6848 (mt) REVERT: F 79 MET cc_start: 0.5422 (mmm) cc_final: 0.5153 (mmm) outliers start: 81 outliers final: 68 residues processed: 343 average time/residue: 0.8217 time to fit residues: 435.8986 Evaluate side-chains 339 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 268 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 622 ASP 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 857 LEU Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 266 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN C1257 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30045 Z= 0.246 Angle : 0.682 9.061 41067 Z= 0.373 Chirality : 0.043 0.179 4675 Planarity : 0.005 0.054 4992 Dihedral : 18.451 177.249 5048 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.79 % Favored : 91.07 % Rotamer: Outliers : 2.45 % Allowed : 15.52 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.70 (0.13), residues: 3437 helix: -0.56 (0.14), residues: 1285 sheet: -2.08 (0.24), residues: 375 loop : -2.75 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.011 0.001 HIS F 225 PHE 0.020 0.002 PHE C 156 TYR 0.025 0.002 TYR F 20 ARG 0.006 0.001 ARG D 738 *********************** 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 366 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 294 time to evaluate : 3.483 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: C 628 HIS cc_start: 0.2680 (OUTLIER) cc_final: 0.1744 (p-80) REVERT: D 473 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6619 (t) outliers start: 72 outliers final: 68 residues processed: 354 average time/residue: 0.8390 time to fit residues: 462.1690 Evaluate side-chains 356 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 286 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 780 ARG Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30045 Z= 0.228 Angle : 0.663 9.407 41067 Z= 0.361 Chirality : 0.043 0.170 4675 Planarity : 0.005 0.053 4992 Dihedral : 18.396 177.081 5048 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.98 % Favored : 89.87 % Rotamer: Outliers : 2.45 % Allowed : 15.59 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.46 (0.13), residues: 3437 helix: -0.32 (0.14), residues: 1287 sheet: -1.99 (0.25), residues: 376 loop : -2.64 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.007 0.001 HIS F 225 PHE 0.018 0.002 PHE C 156 TYR 0.027 0.001 TYR F 20 ARG 0.007 0.001 ARG D 738 *********************** 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 365 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 3.495 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: C 546 GLU cc_start: 0.7066 (pm20) cc_final: 0.6673 (pm20) REVERT: C 628 HIS cc_start: 0.2579 (OUTLIER) cc_final: 0.1717 (p-80) REVERT: D 473 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6650 (t) outliers start: 72 outliers final: 62 residues processed: 346 average time/residue: 0.7988 time to fit residues: 433.7669 Evaluate side-chains 341 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 322 optimal weight: 0.1980 chunk 279 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** D 458 ASN ** 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: 0.5514 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30045 Z= 0.205 Angle : 0.652 9.218 41067 Z= 0.354 Chirality : 0.042 0.162 4675 Planarity : 0.005 0.056 4992 Dihedral : 18.332 176.378 5046 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.94 % Favored : 91.91 % Rotamer: Outliers : 2.24 % Allowed : 16.13 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.26 (0.14), residues: 3437 helix: -0.14 (0.14), residues: 1291 sheet: -1.95 (0.25), residues: 365 loop : -2.52 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.006 0.001 HIS F 225 PHE 0.038 0.002 PHE C1323 TYR 0.027 0.001 TYR F 20 ARG 0.007 0.000 ARG D 738 ********************** 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: 66 poor density : 287 time to evaluate : 3.474 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: C 628 HIS cc_start: 0.2438 (OUTLIER) cc_final: 0.1558 (p-80) REVERT: D 473 THR cc_start: 0.6948 (OUTLIER) cc_final: 0.6711 (t) REVERT: D 1019 ASN cc_start: 0.2677 (OUTLIER) cc_final: 0.2309 (m-40) outliers start: 66 outliers final: 58 residues processed: 336 average time/residue: 0.8242 time to fit residues: 431.3027 Evaluate side-chains 337 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 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 = 0.4065 r_free = 0.4065 target = 0.085659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.064065 restraints weight = 516729.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.066525 restraints weight = 315094.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.068220 restraints weight = 224371.301| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30045 Z= 0.237 Angle : 0.663 7.885 41067 Z= 0.361 Chirality : 0.042 0.190 4675 Planarity : 0.005 0.054 4992 Dihedral : 18.309 176.457 5046 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.95 % Favored : 89.90 % Rotamer: Outliers : 2.41 % Allowed : 16.00 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.27 (0.14), residues: 3437 helix: -0.15 (0.14), residues: 1296 sheet: -1.96 (0.25), residues: 369 loop : -2.53 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.006 0.001 HIS F 225 PHE 0.031 0.002 PHE C1323 TYR 0.025 0.001 TYR F 20 ARG 0.007 0.001 ARG D 738 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11054.21 seconds wall clock time: 197 minutes 11.78 seconds (11831.78 seconds total)