Starting phenix.real_space_refine (version: dev) on Mon Feb 20 11:50:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f7f_31487/02_2023/7f7f_31487.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 9046 Classifications: {'peptide': 1135} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 1096} Chain breaks: 3 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.59 Number of scatterers: 12076 At special positions: 0 Unit cell: (148.755, 109.72, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 1 11.99 O 2253 8.00 N 1996 7.00 C 7766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 32.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 221 through 232 removed outlier: 4.596A pdb=" N PHE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.958A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.512A pdb=" N ASP A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.937A pdb=" N GLY A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.510A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.799A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.760A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.509A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.685A pdb=" N LEU A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.004A pdb=" N PHE A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.663A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 removed outlier: 4.226A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.500A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.717A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.997A pdb=" N ALA A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.754A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.693A pdb=" N LEU A1092 " --> pdb=" O ARG A1088 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1121 removed outlier: 3.614A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.672A pdb=" N MET A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1173 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.590A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.628A pdb=" N PHE A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 4.192A pdb=" N LEU A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1255 removed outlier: 3.756A pdb=" N LEU A1255 " --> pdb=" O VAL A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1252 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.666A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1266 through 1287 removed outlier: 3.567A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1275 " --> pdb=" O LEU A1271 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A1276 " --> pdb=" O TRP A1272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1285 " --> pdb=" O SER A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.738A pdb=" N ILE A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 3.507A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.604A pdb=" N VAL A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 3.528A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1418 removed outlier: 3.550A pdb=" N ARG A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 removed outlier: 4.126A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.673A pdb=" N ASP B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.660A pdb=" N ASP B 269 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.713A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.667A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.610A pdb=" N ILE A 409 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 8.227A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 683 removed outlier: 7.829A pdb=" N MET A 677 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 966 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE A 679 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU A 964 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 681 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 960 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 836 through 839 removed outlier: 3.851A pdb=" N ILE A 852 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.769A pdb=" N VAL B 173 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.021A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.612A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 247 hydrogen bonds defined for protein. 690 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: 3.87 Time building geometry restraints manager: 5.34 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: 3684 1.34 - 1.46: 2798 1.46 - 1.58: 5781 1.58 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 12353 Sorted by residual: bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.64e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.488 -0.039 1.45e-02 4.76e+03 7.26e+00 bond pdb=" C VAL A1408 " pdb=" N GLU A1409 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.50e-02 4.44e+03 5.88e+00 bond pdb=" CD LYS A 542 " pdb=" CE LYS A 542 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.30e+00 bond pdb=" CG LYS A 542 " pdb=" CD LYS A 542 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.79e+00 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.52: 176 104.52 - 112.19: 5665 112.19 - 119.87: 5230 119.87 - 127.54: 5552 127.54 - 135.22: 129 Bond angle restraints: 16752 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 112.29 105.99 6.30 9.40e-01 1.13e+00 4.49e+01 angle pdb=" N PHE A1366 " pdb=" CA PHE A1366 " pdb=" C PHE A1366 " ideal model delta sigma weight residual 114.56 107.61 6.95 1.27e+00 6.20e-01 3.00e+01 angle pdb=" C TYR A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C CYS A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 16747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.47: 6927 20.47 - 40.93: 355 40.93 - 61.40: 32 61.40 - 81.86: 2 81.86 - 102.33: 2 Dihedral angle restraints: 7318 sinusoidal: 2954 harmonic: 4364 Sorted by residual: dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual -180.00 -137.75 -42.25 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N LYS A 542 " pdb=" CA LYS A 542 " ideal model delta harmonic sigma weight residual -180.00 -138.58 -41.42 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLN A 233 " pdb=" C GLN A 233 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " ideal model delta harmonic sigma weight residual 180.00 -138.98 -41.02 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 7315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1257 0.058 - 0.116: 474 0.116 - 0.174: 119 0.174 - 0.231: 18 0.231 - 0.289: 5 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CB VAL A 245 " pdb=" CA VAL A 245 " pdb=" CG1 VAL A 245 " pdb=" CG2 VAL A 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE A 406 " pdb=" CA ILE A 406 " pdb=" CG1 ILE A 406 " pdb=" CG2 ILE A 406 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 462 " pdb=" CA ILE A 462 " pdb=" CG1 ILE A 462 " pdb=" CG2 ILE A 462 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1870 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C PHE B 398 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C VAL A1408 " -0.100 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1287 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1288 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1288 " -0.047 5.00e-02 4.00e+02 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 292 2.68 - 3.23: 11016 3.23 - 3.79: 18973 3.79 - 4.34: 25164 4.34 - 4.90: 40361 Nonbonded interactions: 95806 Sorted by model distance: nonbonded pdb=" O THR A 669 " pdb="MG MG A1601 " model vdw 2.121 2.170 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.184 2.440 nonbonded pdb=" O ASP A 667 " pdb=" OG1 THR A 671 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR A1221 " pdb=" OG1 THR A1353 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.262 2.170 ... (remaining 95801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 60 5.16 5 C 7766 2.51 5 N 1996 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.650 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: 6.500 Check model and map are aligned: 0.190 Process input model: 34.560 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.008 0.102 12353 Z= 0.488 Angle : 1.115 11.844 16752 Z= 0.593 Chirality : 0.063 0.289 1873 Planarity : 0.008 0.084 2123 Dihedral : 11.992 102.330 4514 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.32 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -5.60 (0.16), residues: 1487 helix: -4.70 (0.10), residues: 493 sheet: -3.22 (0.37), residues: 128 loop : -3.29 (0.17), residues: 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2885 time to fit residues: 75.3189 Evaluate side-chains 113 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 484 ASN A 556 ASN A 674 GLN A1046 ASN A1061 HIS A1067 ASN A1096 ASN A1209 ASN A1226 ASN A1301 ASN A1307 HIS ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 209 HIS B 330 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 12353 Z= 0.236 Angle : 0.690 7.384 16752 Z= 0.367 Chirality : 0.046 0.186 1873 Planarity : 0.005 0.065 2123 Dihedral : 8.146 101.007 1681 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.67 % Favored : 92.27 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.18), residues: 1487 helix: -3.84 (0.15), residues: 508 sheet: -2.94 (0.38), residues: 145 loop : -2.89 (0.19), residues: 834 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 159 average time/residue: 0.2537 time to fit residues: 58.5424 Evaluate side-chains 123 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1396 time to fit residues: 4.9143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 125 HIS B 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12353 Z= 0.167 Angle : 0.650 13.284 16752 Z= 0.335 Chirality : 0.044 0.183 1873 Planarity : 0.004 0.056 2123 Dihedral : 7.528 100.739 1681 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.17 (0.19), residues: 1487 helix: -3.24 (0.18), residues: 496 sheet: -2.55 (0.41), residues: 141 loop : -2.54 (0.20), residues: 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 158 average time/residue: 0.2260 time to fit residues: 54.4863 Evaluate side-chains 126 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1181 time to fit residues: 4.1130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 144 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 674 GLN A 778 HIS ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12353 Z= 0.191 Angle : 0.627 9.733 16752 Z= 0.325 Chirality : 0.044 0.166 1873 Planarity : 0.004 0.056 2123 Dihedral : 7.253 100.653 1681 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.91 (0.20), residues: 1487 helix: -2.95 (0.19), residues: 497 sheet: -2.58 (0.39), residues: 155 loop : -2.38 (0.21), residues: 835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 146 average time/residue: 0.2501 time to fit residues: 54.6048 Evaluate side-chains 134 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1240 time to fit residues: 5.2893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 12353 Z= 0.203 Angle : 0.631 9.732 16752 Z= 0.325 Chirality : 0.044 0.185 1873 Planarity : 0.004 0.055 2123 Dihedral : 7.080 100.640 1681 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.71 (0.20), residues: 1487 helix: -2.75 (0.20), residues: 498 sheet: -2.47 (0.39), residues: 155 loop : -2.29 (0.21), residues: 834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 141 average time/residue: 0.2375 time to fit residues: 49.8710 Evaluate side-chains 123 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1254 time to fit residues: 3.4392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A1067 ASN ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12353 Z= 0.190 Angle : 0.636 12.394 16752 Z= 0.324 Chirality : 0.044 0.171 1873 Planarity : 0.004 0.055 2123 Dihedral : 6.955 100.578 1681 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -3.58 (0.20), residues: 1487 helix: -2.55 (0.20), residues: 504 sheet: -2.41 (0.40), residues: 156 loop : -2.26 (0.21), residues: 827 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.2456 time to fit residues: 53.0044 Evaluate side-chains 133 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1405 time to fit residues: 4.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 0.0040 chunk 143 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12353 Z= 0.177 Angle : 0.626 9.497 16752 Z= 0.321 Chirality : 0.043 0.217 1873 Planarity : 0.003 0.057 2123 Dihedral : 6.805 100.482 1681 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -3.38 (0.21), residues: 1487 helix: -2.35 (0.21), residues: 510 sheet: -2.25 (0.39), residues: 156 loop : -2.16 (0.21), residues: 821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 141 average time/residue: 0.2484 time to fit residues: 52.6656 Evaluate side-chains 124 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2145 time to fit residues: 3.6351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 0.0060 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12353 Z= 0.173 Angle : 0.614 9.430 16752 Z= 0.314 Chirality : 0.043 0.234 1873 Planarity : 0.003 0.058 2123 Dihedral : 6.721 100.307 1681 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -3.26 (0.21), residues: 1487 helix: -2.19 (0.21), residues: 508 sheet: -2.06 (0.38), residues: 166 loop : -2.17 (0.21), residues: 813 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 141 average time/residue: 0.2473 time to fit residues: 52.8514 Evaluate side-chains 126 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.333 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1938 time to fit residues: 4.1469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 0.0870 chunk 41 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 675 ASN A1330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12353 Z= 0.210 Angle : 0.636 9.179 16752 Z= 0.325 Chirality : 0.044 0.222 1873 Planarity : 0.004 0.059 2123 Dihedral : 6.737 100.413 1681 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -3.24 (0.21), residues: 1487 helix: -2.12 (0.22), residues: 507 sheet: -2.08 (0.38), residues: 167 loop : -2.18 (0.21), residues: 813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 0.2474 time to fit residues: 48.7621 Evaluate side-chains 126 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.467 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2049 time to fit residues: 4.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 148 optimal weight: 0.0670 chunk 136 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 763 GLN A 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12353 Z= 0.188 Angle : 0.626 9.572 16752 Z= 0.319 Chirality : 0.044 0.208 1873 Planarity : 0.003 0.059 2123 Dihedral : 6.661 100.253 1681 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.15 (0.21), residues: 1487 helix: -2.02 (0.22), residues: 508 sheet: -1.93 (0.39), residues: 166 loop : -2.17 (0.21), residues: 813 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.2415 time to fit residues: 45.0803 Evaluate side-chains 120 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.478 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2104 time to fit residues: 3.1506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176877 restraints weight = 14497.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172022 restraints weight = 26093.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170831 restraints weight = 40861.545| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12353 Z= 0.232 Angle : 0.641 9.440 16752 Z= 0.327 Chirality : 0.045 0.208 1873 Planarity : 0.004 0.059 2123 Dihedral : 6.743 100.438 1681 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.15 (0.21), residues: 1487 helix: -2.02 (0.22), residues: 508 sheet: -1.99 (0.39), residues: 162 loop : -2.17 (0.21), residues: 817 =============================================================================== Job complete usr+sys time: 2286.62 seconds wall clock time: 43 minutes 15.28 seconds (2595.28 seconds total)