Starting phenix.real_space_refine on Fri Mar 15 09:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mpe_23932/03_2024/7mpe_23932.pdb" } resolution = 3.2 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= 0.009 sd= 0.113 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7251 2.51 5 N 1873 2.21 5 O 2039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 785": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A TYR 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1035": "NH1" <-> "NH2" Residue "A PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A TYR 1246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1248": "OD1" <-> "OD2" Residue "A GLU 1284": "OE1" <-> "OE2" Residue "A PHE 1320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1383": "OE1" <-> "OE2" Residue "A GLU 1405": "OE1" <-> "OE2" Residue "A ASP 1475": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11214 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11214 Classifications: {'peptide': 1428} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 43, 'TRANS': 1384} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 6.23, per 1000 atoms: 0.56 Number of scatterers: 11214 At special positions: 0 Unit cell: (84.46, 141.11, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2039 8.00 N 1873 7.00 C 7251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 66.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 4.065A pdb=" N ASP A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 57 removed outlier: 3.668A pdb=" N SER A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.692A pdb=" N ALA A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.750A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 161 removed outlier: 4.185A pdb=" N TRP A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 143 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.617A pdb=" N SER A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.621A pdb=" N THR A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 4.159A pdb=" N LEU A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.648A pdb=" N THR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 302 removed outlier: 4.139A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 323 removed outlier: 3.597A pdb=" N SER A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.854A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.645A pdb=" N GLY A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.804A pdb=" N TYR A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.877A pdb=" N SER A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 4.137A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 5.349A pdb=" N ASN A 424 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A 425 " --> pdb=" O TRP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.877A pdb=" N SER A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.003A pdb=" N ILE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 493 removed outlier: 3.586A pdb=" N ILE A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 503 through 518 removed outlier: 4.765A pdb=" N LYS A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 554 removed outlier: 3.552A pdb=" N VAL A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 4.282A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 550 " --> pdb=" O CYS A 546 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 580 removed outlier: 3.585A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Proline residue: A 566 - end of helix removed outlier: 3.527A pdb=" N THR A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix removed outlier: 3.544A pdb=" N ILE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.751A pdb=" N LEU A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.958A pdb=" N LYS A 743 " --> pdb=" O ASP A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.553A pdb=" N ARG A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.990A pdb=" N ALA A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 removed outlier: 4.499A pdb=" N GLU A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 794 " --> pdb=" O HIS A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 947 through 982 removed outlier: 4.380A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 954 " --> pdb=" O SER A 950 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1016 removed outlier: 3.560A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A1001 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1034 removed outlier: 4.011A pdb=" N TYR A1024 " --> pdb=" O HIS A1020 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A1027 " --> pdb=" O LYS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.725A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.536A pdb=" N ILE A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1055 Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.755A pdb=" N SER A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1089 removed outlier: 3.503A pdb=" N LYS A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1126 removed outlier: 3.893A pdb=" N ILE A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 3.656A pdb=" N PHE A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1138 removed outlier: 3.875A pdb=" N GLU A1134 " --> pdb=" O SER A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1184 removed outlier: 3.840A pdb=" N PHE A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A1162 " --> pdb=" O ARG A1158 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A1165 " --> pdb=" O ASN A1161 " (cutoff:3.500A) Proline residue: A1168 - end of helix removed outlier: 3.813A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1201 removed outlier: 3.757A pdb=" N LEU A1189 " --> pdb=" O SER A1185 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A1198 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 3.745A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A1212 " --> pdb=" O MET A1208 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1213 " --> pdb=" O VAL A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1220 No H-bonds generated for 'chain 'A' and resid 1218 through 1220' Processing helix chain 'A' and resid 1221 through 1247 removed outlier: 3.507A pdb=" N TRP A1225 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A1226 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A1230 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A1241 " --> pdb=" O ILE A1237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1346 removed outlier: 3.531A pdb=" N LEU A1345 " --> pdb=" O GLY A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1349 No H-bonds generated for 'chain 'A' and resid 1347 through 1349' Processing helix chain 'A' and resid 1363 through 1367 Processing helix chain 'A' and resid 1374 through 1385 Processing helix chain 'A' and resid 1388 through 1395 removed outlier: 4.066A pdb=" N LEU A1392 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET A1394 " --> pdb=" O HIS A1390 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1426 removed outlier: 3.960A pdb=" N LEU A1417 " --> pdb=" O GLY A1413 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1426 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1456 Processing helix chain 'A' and resid 1467 through 1472 removed outlier: 3.933A pdb=" N ILE A1471 " --> pdb=" O ARG A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1496 Processing helix chain 'A' and resid 1500 through 1510 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 3.584A pdb=" N VAL A 689 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 646 through 654 removed outlier: 4.293A pdb=" N LYS A 647 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 632 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 649 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE A 651 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 628 " --> pdb=" O PHE A 651 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696 removed outlier: 3.689A pdb=" N VAL A 696 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 777 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA A 824 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS A 660 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 826 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 662 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 823 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN A 834 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 825 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1292 removed outlier: 6.049A pdb=" N LYS A1290 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR A1279 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A1277 " --> pdb=" O GLU A1327 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A1327 " --> pdb=" O TYR A1277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1350 through 1352 removed outlier: 3.814A pdb=" N ILE A1352 " --> pdb=" O VAL A1432 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1302 " --> pdb=" O THR A1463 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A1480 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A1305 " --> pdb=" O LEU A1480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 591 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3561 1.34 - 1.46: 2257 1.46 - 1.58: 5542 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 11443 Sorted by residual: bond pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 1.98e+00 bond pdb=" CG LEU A 390 " pdb=" CD1 LEU A 390 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" N GLU A 641 " pdb=" CA GLU A 641 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.95e-02 2.63e+03 1.83e+00 bond pdb=" C PRO A1262 " pdb=" N PRO A1263 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" CB ILE A 183 " pdb=" CG2 ILE A 183 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 ... (remaining 11438 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.84: 175 105.84 - 112.92: 6286 112.92 - 120.00: 4120 120.00 - 127.09: 4840 127.09 - 134.17: 109 Bond angle restraints: 15530 Sorted by residual: angle pdb=" CB ARG A1459 " pdb=" CG ARG A1459 " pdb=" CD ARG A1459 " ideal model delta sigma weight residual 111.30 122.57 -11.27 2.30e+00 1.89e-01 2.40e+01 angle pdb=" C PRO A 640 " pdb=" N GLU A 641 " pdb=" CA GLU A 641 " ideal model delta sigma weight residual 124.82 132.51 -7.69 1.78e+00 3.16e-01 1.87e+01 angle pdb=" C THR A 110 " pdb=" N MET A 111 " pdb=" CA MET A 111 " ideal model delta sigma weight residual 120.31 114.80 5.51 1.52e+00 4.33e-01 1.32e+01 angle pdb=" CA MET A 111 " pdb=" CB MET A 111 " pdb=" CG MET A 111 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N PRO A1262 " pdb=" CA PRO A1262 " pdb=" C PRO A1262 " ideal model delta sigma weight residual 110.70 115.01 -4.31 1.22e+00 6.72e-01 1.25e+01 ... (remaining 15525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6115 17.92 - 35.84: 610 35.84 - 53.76: 75 53.76 - 71.68: 17 71.68 - 89.60: 8 Dihedral angle restraints: 6825 sinusoidal: 2646 harmonic: 4179 Sorted by residual: dihedral pdb=" CA GLU A1265 " pdb=" C GLU A1265 " pdb=" N TRP A1266 " pdb=" CA TRP A1266 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ASP A1458 " pdb=" C ASP A1458 " pdb=" N ARG A1459 " pdb=" CA ARG A1459 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU A 347 " pdb=" C LEU A 347 " pdb=" N ILE A 348 " pdb=" CA ILE A 348 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1259 0.044 - 0.087: 472 0.087 - 0.131: 76 0.131 - 0.175: 10 0.175 - 0.218: 3 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB ILE A1226 " pdb=" CA ILE A1226 " pdb=" CG1 ILE A1226 " pdb=" CG2 ILE A1226 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 183 " pdb=" CA ILE A 183 " pdb=" CG1 ILE A 183 " pdb=" CG2 ILE A 183 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA ARG A1459 " pdb=" N ARG A1459 " pdb=" C ARG A1459 " pdb=" CB ARG A1459 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 1817 not shown) Planarity restraints: 1943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 429 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 430 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 565 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO A 566 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 947 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 948 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.025 5.00e-02 4.00e+02 ... (remaining 1940 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 591 2.72 - 3.26: 12589 3.26 - 3.81: 18347 3.81 - 4.35: 22395 4.35 - 4.90: 37451 Nonbonded interactions: 91373 Sorted by model distance: nonbonded pdb=" OG1 THR A 836 " pdb=" OD1 ASP A 838 " model vdw 2.174 2.440 nonbonded pdb=" O ASP A 412 " pdb=" OG SER A 594 " model vdw 2.183 2.440 nonbonded pdb=" OG SER A 41 " pdb=" OE2 GLU A 142 " model vdw 2.217 2.440 nonbonded pdb=" O LEU A1494 " pdb=" OG SER A1500 " model vdw 2.236 2.440 nonbonded pdb=" O GLY A 20 " pdb=" OG1 THR A 29 " model vdw 2.240 2.440 ... (remaining 91368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 32.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.005 0.046 11443 Z= 0.290 Angle : 0.689 11.266 15530 Z= 0.373 Chirality : 0.044 0.218 1820 Planarity : 0.004 0.061 1943 Dihedral : 14.097 89.603 4121 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.21), residues: 1420 helix: -0.97 (0.17), residues: 859 sheet: -3.02 (0.51), residues: 65 loop : -2.58 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 70 HIS 0.007 0.001 HIS A1347 PHE 0.024 0.002 PHE A 464 TYR 0.027 0.002 TYR A1215 ARG 0.012 0.001 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8046 (pmm) cc_final: 0.7680 (pmm) REVERT: A 237 TYR cc_start: 0.7281 (m-80) cc_final: 0.6564 (m-80) REVERT: A 254 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8131 (mt-10) REVERT: A 635 LEU cc_start: 0.8682 (pt) cc_final: 0.8476 (pt) REVERT: A 777 ASP cc_start: 0.8057 (t70) cc_final: 0.7765 (t0) REVERT: A 962 MET cc_start: 0.8288 (tpt) cc_final: 0.8048 (tpp) REVERT: A 1048 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7057 (ptp-170) REVERT: A 1394 MET cc_start: 0.7373 (mpp) cc_final: 0.7057 (mpp) REVERT: A 1446 LYS cc_start: 0.9070 (pttm) cc_final: 0.8847 (pttm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2382 time to fit residues: 62.3583 Evaluate side-chains 142 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN A1386 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11443 Z= 0.164 Angle : 0.568 7.567 15530 Z= 0.296 Chirality : 0.040 0.166 1820 Planarity : 0.004 0.054 1943 Dihedral : 5.001 23.923 1536 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.07 % Allowed : 9.79 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1420 helix: -0.23 (0.18), residues: 892 sheet: -2.75 (0.53), residues: 65 loop : -2.31 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 70 HIS 0.007 0.001 HIS A 786 PHE 0.019 0.001 PHE A 464 TYR 0.024 0.001 TYR A1105 ARG 0.007 0.000 ARG A1459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8110 (pmm) cc_final: 0.7772 (pmm) REVERT: A 230 MET cc_start: 0.7332 (mmt) cc_final: 0.6709 (mmt) REVERT: A 237 TYR cc_start: 0.7295 (m-80) cc_final: 0.6757 (m-80) REVERT: A 631 ASP cc_start: 0.8457 (t70) cc_final: 0.8131 (t0) REVERT: A 635 LEU cc_start: 0.8497 (pt) cc_final: 0.7953 (tp) REVERT: A 723 GLU cc_start: 0.8592 (mp0) cc_final: 0.8305 (mp0) REVERT: A 777 ASP cc_start: 0.7998 (t70) cc_final: 0.7640 (t0) REVERT: A 1445 ASP cc_start: 0.8286 (t0) cc_final: 0.7825 (m-30) outliers start: 13 outliers final: 7 residues processed: 175 average time/residue: 0.2284 time to fit residues: 57.7242 Evaluate side-chains 151 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1386 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 128 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A 833 GLN A1386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11443 Z= 0.178 Angle : 0.543 6.616 15530 Z= 0.282 Chirality : 0.040 0.162 1820 Planarity : 0.004 0.050 1943 Dihedral : 4.768 22.665 1536 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.06 % Allowed : 12.02 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1420 helix: 0.05 (0.18), residues: 882 sheet: -2.70 (0.62), residues: 55 loop : -2.15 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 70 HIS 0.010 0.001 HIS A1386 PHE 0.021 0.001 PHE A1040 TYR 0.019 0.001 TYR A1105 ARG 0.005 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7606 (t80) cc_final: 0.7401 (t80) REVERT: A 45 MET cc_start: 0.7433 (mmm) cc_final: 0.6827 (tpp) REVERT: A 237 TYR cc_start: 0.7353 (m-80) cc_final: 0.6776 (m-80) REVERT: A 248 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8031 (tpp80) REVERT: A 535 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 631 ASP cc_start: 0.8569 (t70) cc_final: 0.8232 (t0) REVERT: A 635 LEU cc_start: 0.8496 (pt) cc_final: 0.7916 (tp) REVERT: A 723 GLU cc_start: 0.8586 (mp0) cc_final: 0.8312 (mp0) REVERT: A 777 ASP cc_start: 0.7838 (t70) cc_final: 0.7456 (t70) REVERT: A 1213 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 1459 ARG cc_start: 0.6810 (mmm160) cc_final: 0.6444 (mmp80) outliers start: 25 outliers final: 16 residues processed: 174 average time/residue: 0.2273 time to fit residues: 58.0622 Evaluate side-chains 162 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 67 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 786 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11443 Z= 0.167 Angle : 0.532 6.530 15530 Z= 0.276 Chirality : 0.039 0.156 1820 Planarity : 0.004 0.045 1943 Dihedral : 4.573 21.702 1536 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.22 % Allowed : 14.65 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1420 helix: 0.23 (0.18), residues: 880 sheet: -2.51 (0.63), residues: 55 loop : -2.05 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 70 HIS 0.018 0.001 HIS A 786 PHE 0.014 0.001 PHE A 464 TYR 0.020 0.001 TYR A1105 ARG 0.010 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7430 (mmm) cc_final: 0.6778 (tpp) REVERT: A 237 TYR cc_start: 0.7293 (m-80) cc_final: 0.6796 (m-80) REVERT: A 535 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 631 ASP cc_start: 0.8534 (t70) cc_final: 0.8210 (t0) REVERT: A 635 LEU cc_start: 0.8451 (pt) cc_final: 0.7871 (tp) REVERT: A 777 ASP cc_start: 0.8234 (t70) cc_final: 0.7732 (t0) REVERT: A 1032 SER cc_start: 0.8606 (t) cc_final: 0.8311 (t) REVERT: A 1334 ASN cc_start: 0.8813 (p0) cc_final: 0.8253 (m110) REVERT: A 1459 ARG cc_start: 0.6818 (mmm160) cc_final: 0.6509 (mmp80) outliers start: 27 outliers final: 18 residues processed: 177 average time/residue: 0.2261 time to fit residues: 58.6345 Evaluate side-chains 166 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11443 Z= 0.316 Angle : 0.606 6.423 15530 Z= 0.315 Chirality : 0.042 0.180 1820 Planarity : 0.004 0.042 1943 Dihedral : 4.799 21.224 1536 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.21 % Allowed : 15.72 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1420 helix: 0.02 (0.18), residues: 883 sheet: -2.39 (0.63), residues: 55 loop : -2.05 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 70 HIS 0.003 0.001 HIS A 297 PHE 0.016 0.002 PHE A 44 TYR 0.020 0.001 TYR A1105 ARG 0.005 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7404 (mmm) cc_final: 0.7196 (tpt) REVERT: A 230 MET cc_start: 0.7391 (mmt) cc_final: 0.6843 (mmt) REVERT: A 237 TYR cc_start: 0.7268 (m-80) cc_final: 0.6888 (m-80) REVERT: A 448 MET cc_start: 0.8210 (ptp) cc_final: 0.7980 (ptp) REVERT: A 535 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 631 ASP cc_start: 0.8521 (t70) cc_final: 0.8228 (t0) REVERT: A 635 LEU cc_start: 0.8596 (pt) cc_final: 0.7996 (tp) REVERT: A 723 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: A 777 ASP cc_start: 0.8106 (t70) cc_final: 0.7582 (t0) REVERT: A 789 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8469 (mtm-85) outliers start: 39 outliers final: 31 residues processed: 183 average time/residue: 0.2137 time to fit residues: 57.3098 Evaluate side-chains 174 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11443 Z= 0.174 Angle : 0.550 9.294 15530 Z= 0.283 Chirality : 0.040 0.151 1820 Planarity : 0.003 0.041 1943 Dihedral : 4.534 20.941 1536 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.30 % Allowed : 18.27 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1420 helix: 0.30 (0.18), residues: 881 sheet: -2.30 (0.64), residues: 55 loop : -1.94 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 70 HIS 0.004 0.001 HIS A 690 PHE 0.015 0.001 PHE A 576 TYR 0.022 0.001 TYR A1105 ARG 0.005 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7332 (mmm) cc_final: 0.7122 (tpt) REVERT: A 237 TYR cc_start: 0.7248 (m-80) cc_final: 0.6855 (m-80) REVERT: A 448 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7919 (ptt) REVERT: A 535 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 631 ASP cc_start: 0.8511 (t70) cc_final: 0.7840 (t0) REVERT: A 635 LEU cc_start: 0.8512 (pt) cc_final: 0.8002 (tp) REVERT: A 723 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: A 777 ASP cc_start: 0.7905 (t70) cc_final: 0.7446 (t0) REVERT: A 1032 SER cc_start: 0.8522 (t) cc_final: 0.8291 (t) REVERT: A 1445 ASP cc_start: 0.8221 (t0) cc_final: 0.7766 (m-30) outliers start: 28 outliers final: 20 residues processed: 174 average time/residue: 0.2132 time to fit residues: 54.6876 Evaluate side-chains 167 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 85 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11443 Z= 0.192 Angle : 0.561 9.443 15530 Z= 0.287 Chirality : 0.040 0.175 1820 Planarity : 0.004 0.037 1943 Dihedral : 4.481 20.124 1536 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.88 % Allowed : 18.44 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1420 helix: 0.36 (0.18), residues: 885 sheet: -2.26 (0.64), residues: 55 loop : -1.91 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 70 HIS 0.003 0.001 HIS A 786 PHE 0.017 0.001 PHE A1040 TYR 0.020 0.001 TYR A1105 ARG 0.006 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7346 (mmm) cc_final: 0.7144 (tpt) REVERT: A 237 TYR cc_start: 0.7219 (m-80) cc_final: 0.6832 (m-80) REVERT: A 448 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7861 (ptt) REVERT: A 535 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8567 (tm-30) REVERT: A 631 ASP cc_start: 0.8416 (t70) cc_final: 0.8079 (t0) REVERT: A 635 LEU cc_start: 0.8529 (pt) cc_final: 0.8003 (tp) REVERT: A 722 TYR cc_start: 0.8241 (t80) cc_final: 0.8035 (t80) REVERT: A 723 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: A 777 ASP cc_start: 0.8068 (t70) cc_final: 0.7571 (t0) outliers start: 35 outliers final: 28 residues processed: 172 average time/residue: 0.2056 time to fit residues: 52.6535 Evaluate side-chains 177 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11443 Z= 0.159 Angle : 0.546 9.262 15530 Z= 0.278 Chirality : 0.040 0.162 1820 Planarity : 0.003 0.036 1943 Dihedral : 4.350 19.572 1536 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.55 % Allowed : 19.18 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1420 helix: 0.53 (0.18), residues: 888 sheet: -2.15 (0.61), residues: 67 loop : -1.97 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 70 HIS 0.002 0.001 HIS A1390 PHE 0.014 0.001 PHE A 576 TYR 0.019 0.001 TYR A1105 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7306 (mmm) cc_final: 0.7102 (tpt) REVERT: A 178 ILE cc_start: 0.9115 (tt) cc_final: 0.8649 (pt) REVERT: A 237 TYR cc_start: 0.7145 (m-80) cc_final: 0.6907 (m-80) REVERT: A 535 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 631 ASP cc_start: 0.8414 (t70) cc_final: 0.8065 (t0) REVERT: A 635 LEU cc_start: 0.8521 (pt) cc_final: 0.8062 (tp) REVERT: A 723 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: A 777 ASP cc_start: 0.8241 (t70) cc_final: 0.7857 (t0) outliers start: 31 outliers final: 26 residues processed: 175 average time/residue: 0.2081 time to fit residues: 54.2169 Evaluate side-chains 171 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN A 786 HIS ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11443 Z= 0.263 Angle : 0.594 8.976 15530 Z= 0.303 Chirality : 0.042 0.158 1820 Planarity : 0.004 0.033 1943 Dihedral : 4.497 19.295 1536 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.88 % Allowed : 19.34 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1420 helix: 0.38 (0.18), residues: 888 sheet: -2.25 (0.60), residues: 67 loop : -1.96 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 70 HIS 0.007 0.001 HIS A 786 PHE 0.013 0.001 PHE A 44 TYR 0.020 0.001 TYR A1105 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7355 (mmm) cc_final: 0.7119 (tpt) REVERT: A 237 TYR cc_start: 0.7231 (m-80) cc_final: 0.6877 (m-80) REVERT: A 535 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 631 ASP cc_start: 0.8417 (t70) cc_final: 0.8094 (t0) REVERT: A 635 LEU cc_start: 0.8603 (pt) cc_final: 0.8065 (tp) REVERT: A 723 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: A 777 ASP cc_start: 0.8161 (t70) cc_final: 0.7680 (t0) REVERT: A 1070 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8199 (mm-40) outliers start: 35 outliers final: 33 residues processed: 172 average time/residue: 0.2183 time to fit residues: 55.4785 Evaluate side-chains 179 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 120 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 11443 Z= 0.239 Angle : 0.877 59.189 15530 Z= 0.507 Chirality : 0.058 1.689 1820 Planarity : 0.006 0.172 1943 Dihedral : 4.541 25.131 1536 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.88 % Allowed : 19.42 % Favored : 77.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1420 helix: 0.40 (0.18), residues: 888 sheet: -2.26 (0.59), residues: 67 loop : -1.95 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 70 HIS 0.273 0.008 HIS A 786 PHE 0.013 0.001 PHE A 44 TYR 0.021 0.001 TYR A1105 ARG 0.007 0.000 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7351 (mmm) cc_final: 0.7075 (tpt) REVERT: A 237 TYR cc_start: 0.7226 (m-80) cc_final: 0.6867 (m-80) REVERT: A 535 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 631 ASP cc_start: 0.8412 (t70) cc_final: 0.8091 (t0) REVERT: A 635 LEU cc_start: 0.8603 (pt) cc_final: 0.8062 (tp) REVERT: A 723 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: A 777 ASP cc_start: 0.8150 (t70) cc_final: 0.7677 (t0) REVERT: A 786 HIS cc_start: 0.9183 (OUTLIER) cc_final: 0.8726 (t-90) REVERT: A 1070 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8171 (mm-40) REVERT: A 1218 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7969 (mm-40) outliers start: 35 outliers final: 31 residues processed: 166 average time/residue: 0.2124 time to fit residues: 52.9963 Evaluate side-chains 180 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1215 TYR Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1221 GLN Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.0050 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 50.0000 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096966 restraints weight = 16515.175| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.05 r_work: 0.3231 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 11443 Z= 0.239 Angle : 0.877 59.189 15530 Z= 0.507 Chirality : 0.058 1.689 1820 Planarity : 0.006 0.172 1943 Dihedral : 4.541 25.131 1536 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.80 % Allowed : 19.51 % Favored : 77.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1420 helix: 0.40 (0.18), residues: 888 sheet: -2.26 (0.59), residues: 67 loop : -1.95 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 70 HIS 0.273 0.008 HIS A 786 PHE 0.013 0.001 PHE A 44 TYR 0.021 0.001 TYR A1105 ARG 0.007 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.52 seconds wall clock time: 42 minutes 55.03 seconds (2575.03 seconds total)